Cyclophilin A
Homo sapiens
State in the Current Structure
| Assembly | Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Associated Components | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|
| 1 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain A； UniProt 1–164 | Not recorded | HIV-1 Capsid × 1 （Q72497） | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K | Resolution 1.70 Å R-free 0.230 |
| 2 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain B； UniProt 1–164 | Not recorded | HIV-1 Capsid × 1 （Q72497） | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K | Resolution 1.70 Å R-free 0.230 |
| 3 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain E； UniProt 1–164 | Not recorded | HIV-1 Capsid × 1 （Q72497） | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K | Resolution 1.70 Å R-free 0.230 |
| 4 | Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count | Chain F； UniProt 1–164 | Not recorded | HIV-1 Capsid × 1 （Q72497） | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K | Resolution 1.70 Å R-free 0.230 |
Other States of the Same Protein in the Database
Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.
| Other PDB | Difference from Current Entry 1M9X | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1AK4 HUMAN CYCLOPHILIN A BOUND TO THE AMINO-TERMINAL DOMAIN OF HIV-1 CAPSID Deposited 1997-05-28 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；THE PROTEIN SOLUTION WAS 0.25 MM CYPA AND 0.25 MM CA(151) IN 10 MM TRISHCL (PH 8.0) AND 1 MM 2-MERCAPTOETHANOL. THE RESERVOIR SOLUTION WAS 1ML OF 1.0 M LICL, 0.1 M BICINE (PH 7.0), AND 22% POLYETHYLENE GLYCOL 8000. THE INITIAL DROP WAS 6 MICROL OF A 1:1 MIX OF PROTEIN AND RESERVOIR SOLUTIONS.
|
Resolution 2.36 Å R-free 0.306 |
| 1AK4 HUMAN CYCLOPHILIN A BOUND TO THE AMINO-TERMINAL DOMAIN OF HIV-1 CAPSID Deposited 1997-05-28 | Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；THE PROTEIN SOLUTION WAS 0.25 MM CYPA AND 0.25 MM CA(151) IN 10 MM TRISHCL (PH 8.0) AND 1 MM 2-MERCAPTOETHANOL. THE RESERVOIR SOLUTION WAS 1ML OF 1.0 M LICL, 0.1 M BICINE (PH 7.0), AND 22% POLYETHYLENE GLYCOL 8000. THE INITIAL DROP WAS 6 MICROL OF A 1:1 MIX OF PROTEIN AND RESERVOIR SOLUTIONS.
|
Resolution 2.36 Å R-free 0.306 |
| 1AWQ CYPA COMPLEXED WITH HAGPIA (PSEUDO-SYMMETRIC MONOMER) Deposited 1997-10-04 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 1.58 Å R-free 0.433 |
| 1AWR CYPA COMPLEXED WITH HAGPIA Deposited 1997-10-04 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 1.58 Å R-free 0.461 |
| 1AWR CYPA COMPLEXED WITH HAGPIA Deposited 1997-10-04 | Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 1.58 Å R-free 0.461 |
| 1AWR CYPA COMPLEXED WITH HAGPIA Deposited 1997-10-04 | Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 1.58 Å R-free 0.461 |
| 1AWR CYPA COMPLEXED WITH HAGPIA Deposited 1997-10-04 | Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 1.58 Å R-free 0.461 |
| 1AWR CYPA COMPLEXED WITH HAGPIA Deposited 1997-10-04 | Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 1.58 Å R-free 0.461 |
| 1AWR CYPA COMPLEXED WITH HAGPIA Deposited 1997-10-04 | Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 1.58 Å R-free 0.461 |
| 1AWS SECYPA COMPLEXED WITH HAGPIA (PSEUDO-SYMMETRIC MONOMER) Deposited 1997-10-04 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Mutation：SELENO-METHIONINE SUBSTITUTED Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.55 Å R-free 0.337 |
| 1AWT SECYPA COMPLEXED WITH HAGPIA Deposited 1997-10-05 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Mutation：SELENO-METHIONINE SUBSTITUTED Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.55 Å R-free 0.465 |
| 1AWT SECYPA COMPLEXED WITH HAGPIA Deposited 1997-10-05 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–164（164 aa）
|
Mutation：SELENO-METHIONINE SUBSTITUTED Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.55 Å R-free 0.465 |
| 1AWT SECYPA COMPLEXED WITH HAGPIA Deposited 1997-10-05 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
1–164（164 aa）
|
Mutation：SELENO-METHIONINE SUBSTITUTED Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.55 Å R-free 0.465 |
| 1AWT SECYPA COMPLEXED WITH HAGPIA Deposited 1997-10-05 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–164（164 aa）
|
Mutation：SELENO-METHIONINE SUBSTITUTED Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.55 Å R-free 0.465 |
| 1AWT SECYPA COMPLEXED WITH HAGPIA Deposited 1997-10-05 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–164（164 aa）
|
Mutation：SELENO-METHIONINE SUBSTITUTED Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.55 Å R-free 0.465 |
| 1AWT SECYPA COMPLEXED WITH HAGPIA Deposited 1997-10-05 | Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
1–164（164 aa）
|
Mutation：SELENO-METHIONINE SUBSTITUTED Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.55 Å R-free 0.465 |
| 1AWU CYPA COMPLEXED WITH HVGPIA (PSEUDO-SYMMETRIC MONOMER) Deposited 1997-10-05 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.34 Å R-free 0.351 |
| 1AWV CYPA COMPLEXED WITH HVGPIA Deposited 1997-10-05 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.34 Å R-free 0.460 |
| 1AWV CYPA COMPLEXED WITH HVGPIA Deposited 1997-10-05 | Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.34 Å R-free 0.460 |
| 1AWV CYPA COMPLEXED WITH HVGPIA Deposited 1997-10-05 | Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.34 Å R-free 0.460 |
| 1AWV CYPA COMPLEXED WITH HVGPIA Deposited 1997-10-05 | Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.34 Å R-free 0.460 |
| 1AWV CYPA COMPLEXED WITH HVGPIA Deposited 1997-10-05 | Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.34 Å R-free 0.460 |
| 1AWV CYPA COMPLEXED WITH HVGPIA Deposited 1997-10-05 | Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.4；pH 8.4
|
Resolution 2.34 Å R-free 0.460 |
| 1BCK HUMAN CYCLOPHILIN A COMPLEXED WITH 2-THR CYCLOSPORIN Deposited 1998-04-30 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；PH 8.0
|
Resolution 1.80 Å |
| 1CWF HUMAN CYCLOPHILIN A COMPLEXED WITH 2-VAL CYCLOSPORIN Deposited 1998-04-30 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.86 Å |
| 1CWH HUMAN CYCLOPHILIN A COMPLEXED WITH 3-D-SER CYCLOSPORIN Deposited 1998-05-07 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；PH 8.0
|
Resolution 1.86 Å |
| 1CWI HUMAN CYCLOPHILIN A COMPLEXED WITH 2-VAL 3-(N-METHYL)-D-ALANINE CYCLOSPORIN Deposited 1998-05-25 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；PH 8.0
|
Resolution 1.90 Å |
| 1CWM HUMAN CYCLOPHILIN A COMPLEXED WITH 4 MEILE CYCLOSPORIN Deposited 1998-05-26 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；PH 8.0
|
Resolution 2.00 Å |
| 1CWO HUMAN CYCLOPHILIN A COMPLEXED WITH THR2, LEU5, D-HIV8, LEU10 CYCLOSPORIN Deposited 1998-06-05 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.2；PH 8.2
|
Resolution 1.86 Å |
| 1FGL Cyclophilin A complexed with a fragment of HIV-1 GAG protein Deposited 1996-11-18 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.80 Å R-free 0.256 |
| 1M63 Crystal structure of calcineurin-cyclophilin-cyclosporin shows common but distinct recognition of immunophilin-drug complexes Deposited 2002-07-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain C
0–164（165 aa）
Chain G
0–164（165 aa）
|
Not recorded | ZN ZINC ION × 2 FE FE (III) ION × 2 CA CALCIUM ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；0.1 M NA CACODYLATE, 0.2 M MGCL2, 13% PEG8000, 2.5% ETHANOL, PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 295K
|
Resolution 2.80 Å R-free 0.322 |
| 1M9C X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type Complex. Deposited 2002-07-28 | Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 2.00 Å R-free 0.259 |
| 1M9C X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type Complex. Deposited 2002-07-28 | Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 2.00 Å R-free 0.259 |
| 1M9D X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) O-type chimera Complex. Deposited 2002-07-28 | Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.90 Å R-free 0.232 |
| 1M9D X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) O-type chimera Complex. Deposited 2002-07-28 | Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.90 Å R-free 0.232 |
| 1M9E X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A Complex. Deposited 2002-07-28 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–163（163 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.72 Å R-free 0.226 |
| 1M9E X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A Complex. Deposited 2002-07-28 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–163（163 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.72 Å R-free 0.226 |
| 1M9F X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,A88M Complex. Deposited 2002-07-28 | Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.73 Å R-free 0.220 |
| 1M9F X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,A88M Complex. Deposited 2002-07-28 | Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.73 Å R-free 0.220 |
| 1M9Y X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,G89A Complex. Deposited 2002-07-30 | Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.90 Å R-free 0.234 |
| 1M9Y X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,G89A Complex. Deposited 2002-07-30 | Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.90 Å R-free 0.234 |
| 1M9Y X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,G89A Complex. Deposited 2002-07-30 | Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.90 Å R-free 0.234 |
| 1M9Y X-ray crystal structure of Cyclophilin A/HIV-1 CA N-terminal domain (1-146) M-type H87A,G89A Complex. Deposited 2002-07-30 | Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8.5；294 K；PEG 8K, Bicine, LiCl, Tris, Beta-mercaptoethanol, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K
|
Resolution 1.90 Å R-free 0.234 |
| 1MF8 Crystal Structure of human calcineurin complexed with cyclosporin A and human cyclophilin Deposited 2002-08-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
0–164（165 aa）
|
Not recorded | PO4 PHOSPHATE ION × 1 CA CALCIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.6；12% PEG 4000, 5MM POTASSIUM PHOSPHATE, 75MM SODIUM CITRATE, 15% GLYCEROL, 5MM TRIS, PH 4.6, MICROBATCH, TEMPERATURE 292K
|
Resolution 3.10 Å R-free 0.300 |
| 1NMK The Sanglifehrin-Cyclophilin Interaction: Degradation Work, Synthetic Macrocyclic Analogues, X-ray Crystal Structure and Binding Data Deposited 2003-01-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
0–164（165 aa）
|
Not recorded | SFM (13E,15E)-(3S,6S,9R,10R,11S,12S,18S,21S)-10,12-DIHYDROXY-3-(3-HYDROXYBEN-ZYL)-18-((E)-3-HYDROXY-1-METHYLPROPENYL)-6-ISOPROPYL-11-METHYL-9-(3-OXO-BUTYL)-19-OXA-1,4,7,25-TETRAAZA-BICYCLO[19.3.1]PENTACOSA-13,15-DIENE-2,5,8,20-TETRAONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 6000, tris-HCl, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.189 |
| 1NMK The Sanglifehrin-Cyclophilin Interaction: Degradation Work, Synthetic Macrocyclic Analogues, X-ray Crystal Structure and Binding Data Deposited 2003-01-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
0–164（165 aa）
|
Not recorded | SFM (13E,15E)-(3S,6S,9R,10R,11S,12S,18S,21S)-10,12-DIHYDROXY-3-(3-HYDROXYBEN-ZYL)-18-((E)-3-HYDROXY-1-METHYLPROPENYL)-6-ISOPROPYL-11-METHYL-9-(3-OXO-BUTYL)-19-OXA-1,4,7,25-TETRAAZA-BICYCLO[19.3.1]PENTACOSA-13,15-DIENE-2,5,8,20-TETRAONE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；293 K；PEG 6000, tris-HCl, NaCl, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.10 Å R-free 0.189 |
| 1OCA HUMAN CYCLOPHILIN A, UNLIGATED, NMR, 20 STRUCTURES Deposited 1997-07-07 | Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；299 K
|
Resolution not provided |
| 1W8L Enzymatic and structural characterization of non peptide ligand cyclophilin complexes Deposited 2004-09-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–164（164 aa）
|
Not recorded | 1P3 (3R)-1-ACETYL-3-METHYLPIPERIDINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；100MM TRIS.HCL (PH 8.0), 22% (W/V) PEG 8000, 5% (V/V) DMSO, 0.02% NAN3.
|
Resolution 1.80 Å R-free 0.230 |
| 1W8M Enzymatic and Structural Characterisation of Non Peptide Ligand Cyclophilin Complexes Deposited 2004-09-24 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–164（164 aa）
|
Not recorded | E1P ETHYL OXO(PIPERIDIN-1-YL)ACETATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8；100MM TRIS.HCL (PH 8.0), 22% (W/V) PEG 8000, 5% (V/V) DMSO, 0.02% NAN3.
|
Resolution 1.65 Å R-free 0.186 |
| 1W8V Enzymatic and structural characterization of non peptide ligand cyclophilin complexes Deposited 2004-09-28 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；290 K；14 MG/ML IN HEPES 20MM, NACL 100 MM AND NAN3 0.02 % (W/V). CRYSTALS OF HCYPA WERE GROWN BY VAPOUR DIFFUSION AT 17C BY THE HANGING DROP METHOD IN 100MM TRIS.HCL (PH 8.0), 22% (W/V) PEG 8000, 5% (V/V) DMSO, 0.02% NAN3.
|
Resolution 1.70 Å R-free 0.219 |
| 1YND Structure of human cyclophilin A in complex with the novel immunosuppressant sanglifehrin A at 1.6A resolution Deposited 2005-01-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
0–164（165 aa）
|
Not recorded | SFA SANGLIFEHRIN A × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Mg acetate, Na cacodylate, PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.60 Å R-free 0.185 |
| 1YND Structure of human cyclophilin A in complex with the novel immunosuppressant sanglifehrin A at 1.6A resolution Deposited 2005-01-24 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
0–164（165 aa）
|
Not recorded | SFA SANGLIFEHRIN A × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Mg acetate, Na cacodylate, PEG4000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.60 Å R-free 0.185 |
| 1ZKF Cyrstal Structure of Human Cyclophilin-A in Complex with suc-AGPF-pNA Deposited 2005-05-02 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.2；298 K；Ammonium Sulfate, Tris-HCL, Sodium Azide, Dimethyl Sulfoxide, Glycerol, pH 8.2, VAPOR DIFFUSION, temperature 298K
|
Resolution 2.55 Å R-free 0.210 |
| 1ZKF Cyrstal Structure of Human Cyclophilin-A in Complex with suc-AGPF-pNA Deposited 2005-05-02 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.2；298 K；Ammonium Sulfate, Tris-HCL, Sodium Azide, Dimethyl Sulfoxide, Glycerol, pH 8.2, VAPOR DIFFUSION, temperature 298K
|
Resolution 2.55 Å R-free 0.210 |
| 2ALF crystal structure of human CypA mutant K131A Deposited 2005-08-05 | Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–164（164 aa）
|
Mutation：K131A | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8.5；277 K；Tris Hydrochloride, Polyethylene Glycol 8000, magnesium chloride, pH 8.5, EVAPORATION, temperature 277K
|
Resolution 1.90 Å R-free 0.226 |
| 2CPL SIMILARITIES AND DIFFERENCES BETWEEN HUMAN CYCLOPHILIN A AND OTHER BETA-BARREL STRUCTURES. STRUCTURAL REFINEMENT AT 1.63 ANGSTROMS RESOLUTION Deposited 1992-06-30 | Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.63 Å |
| 2MS4 Cyclophilin a complexed with a fragment of crk-ii Deposited 2014-07-22 | Different construct Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.8；305 K；Ionic strength (raw mmCIF value) 0.1；Pressure ambient
NMR sample composition
0.8 mM [U-100% 13C; U-100% 15N] protein_1, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2MZU Extending the eNOE data set of large proteins by evaluation of NOEs with unresolved diagonals Deposited 2015-02-24 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；299 K；Ionic strength (raw mmCIF value) 0.15；Pressure ambient
NMR sample composition
1.5mm mM [U-100% 13C; U-100% 15N] sodium phosphate, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2N0T Structural ensemble of the enzyme cyclophilin reveals an orchestrated mode of action at atomic resolution Deposited 2015-03-13 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；26 K；Ionic strength (raw mmCIF value) 150；Pressure ambient
NMR sample composition
1.8 mM [U-100% 15N] sodium phosphate, 97% H2O/3% D2O | 97% H2O/3% D2O
|
Resolution not provided |
| 2RMA Crystal structures of cyclophilin A complexed with cyclosporin A and N-methyl-4-[(E)-2-butenyl]-4,4-dimethylthreonine cyclosporin A Deposited 1994-01-07 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric |
Chain A
1–164（164 aa）
Chain C
1–164（164 aa）
Chain E
1–164（164 aa）
Chain G
1–164（164 aa）
Chain I
1–164（164 aa）
Chain K
1–164（164 aa）
Chain M
1–164（164 aa）
Chain O
1–164（164 aa）
Chain Q
1–164（164 aa）
Chain S
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.10 Å |
| 2RMB Crystal structures of cyclophilin A complexed with cyclosporin A and N-methyl-4-[(E)-2-butenyl]-4,4-dimethylthreonine cyclosporin A Deposited 1994-01-07 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric |
Chain A
1–164（164 aa）
Chain C
1–164（164 aa）
Chain E
1–164（164 aa）
Chain G
1–164（164 aa）
Chain I
1–164（164 aa）
Chain K
1–164（164 aa）
Chain M
1–164（164 aa）
Chain O
1–164（164 aa）
Chain Q
1–164（164 aa）
Chain S
1–164（164 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.10 Å |
| 2X25 Free acetyl-CypA orthorhombic form Deposited 2010-01-11 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–165（164 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.20 Å R-free 0.156 |
| 2X2A Free acetyl-CypA trigonal form Deposited 2010-01-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–165（165 aa）
Chain B
1–165（165 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | GOL GLYCEROL × 1 SO4 SULFATE ION × 2 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.40 Å R-free 0.161 |
| 2X2C acetyl-CypA:cyclosporine complex Deposited 2010-01-12 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 20 PDB declaration: eicosameric |
Chain K
1–165（165 aa）
Chain M
1–165（165 aa）
Chain O
1–165（165 aa）
Chain Q
1–165（165 aa）
Chain S
1–165（165 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.41 Å R-free 0.264 |
| 2X2D acetyl-CypA:HIV-1 N-term capsid domain complex Deposited 2010-01-12 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.257 |
| 2X2D acetyl-CypA:HIV-1 N-term capsid domain complex Deposited 2010-01-12 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–165（165 aa）
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 1.95 Å R-free 0.257 |
| 2XGY Complex of Rabbit Endogenous Lentivirus (RELIK)Capsid with Cyclophilin A Deposited 2010-06-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–165（165 aa）
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；16-26% PEG3350, 0.1M HEPES PH 7.5
|
Resolution 1.80 Å R-free 0.187 |
| 3K0M Cryogenic structure of CypA Deposited 2009-09-24 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100 mM HEPES pH 7.5, 22% PEG 3350, 5 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.25 Å R-free 0.149 |
| 3K0N Room temperature structure of CypA Deposited 2009-09-24 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100 mM HEPES pH 7.5, 22% PEG 3350, 5 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.39 Å R-free 0.160 |
| 3K0O Room temperature structure of CypA mutant Ser99Thr Deposited 2009-09-24 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Mutation：S99T | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；1.8 M DL-malic acid, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.55 Å R-free 0.148 |
| 3K0P Cryogenic structure of CypA mutant Ser99Thr Deposited 2009-09-24 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Mutation：S99T | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；1.8 M DL-malic acid, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.65 Å R-free 0.176 |
| 3K0Q Cryogenic structure of CypA mutant Ser99Thr (2) Deposited 2009-09-24 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Mutation：S99T | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100 mM HEPES pH 7.5, 22% PEG 3350, 5 mM TCEP, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.32 Å R-free 0.247 |
| 3K0R Cryogenic structure of CypA mutant Arg55Lys Deposited 2009-09-25 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Mutation：R55K | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；291 K；1.8 M DL-malic acid, pH 7, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.42 Å R-free 0.236 |
| 3RDD Human Cyclophilin A Complexed with an Inhibitor Deposited 2011-04-01 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | EA4 ethyl N-[(4-aminobenzyl)carbamoyl]glycinate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100 mM HEPES, 20% PEG10000, 5% ethanol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.14 Å R-free 0.272 |
| 4IPZ SmBz bound to Cyclophilin A Deposited 2013-01-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–165（165 aa）
|
Not recorded | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6；290 K；1M LiCl, 0.1M MES, 30% (w/v) PEG6000, VAPOR DIFFUSION, SITTING DROP, temperature 290K
|
Resolution 1.67 Å R-free 0.218 |
| 4N1M Structure of Cyclophilin A in complex with GlyPro. Deposited 2013-10-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | GLY GLYCINE × 1 PRO PROLINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；Tris, PEG8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.15 Å R-free 0.163 |
| 4N1N Structure of Cyclophilin A in complex with Benzamide. Deposited 2013-10-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | UNU BENZAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；Tris, PEG8000, pH 8.0, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.50 Å R-free 0.213 |
| 4N1O Structure of Cyclophilin A in complex with Saccharin. Deposited 2013-10-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | LSA 1,2-BENZISOTHIAZOL-3(2H)-ONE 1,1-DIOXIDE × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；Tris, PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.75 Å R-free 0.221 |
| 4N1P Structure of Cyclophilin A in complex with Picolinamide. Deposited 2013-10-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | WM1 pyridine-2-carboxamide × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；Tris, PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.90 Å R-free 0.258 |
| 4N1Q Structure of Cyclophilin A in complex with cyclohexanecarboxamide. Deposited 2013-10-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | WM2 cyclohexanecarboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；Tris, PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.65 Å R-free 0.220 |
| 4N1R Structure of Cyclophilin A in complex with benzenesulfonohydrazide. Deposited 2013-10-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | WM3 benzenesulfonohydrazide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；Tris, PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.80 Å R-free 0.223 |
| 4N1S Structure of Cyclophilin A in complex with benzohydrazide. Deposited 2013-10-04 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | WM4 benzohydrazide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；277 K；Tris, PEG8000, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 1.47 Å R-free 0.224 |
| 4YUG Multiconformer synchrotron model of CypA at 100 K Deposited 2015-03-18 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format.
|
Resolution 1.48 Å R-free 0.183 |
| 4YUH Multiconformer synchrotron model of CypA at 150 K Deposited 2015-03-18 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format.
|
Resolution 1.34 Å R-free 0.156 |
| 4YUI Multiconformer synchrotron model of CypA at 180 K Deposited 2015-03-18 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format.
|
Resolution 1.38 Å R-free 0.175 |
| 4YUJ Multiconformer synchrotron model of CypA at 240 K Deposited 2015-03-18 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format.
|
Resolution 1.42 Å R-free 0.156 |
| 4YUK Multiconformer synchrotron model of CypA at 260 K Deposited 2015-03-18 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format.
|
Resolution 1.48 Å R-free 0.168 |
| 4YUL Multiconformer synchrotron model of CypA at 280 K Deposited 2015-03-18 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format.
|
Resolution 1.42 Å R-free 0.143 |
| 4YUM Multiconformer synchrotron model of CypA at 300 K Deposited 2015-03-18 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format.
|
Resolution 1.50 Å R-free 0.144 |
| 4YUN Multiconformer synchrotron model of CypA at 310 K Deposited 2015-03-18 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format.
|
Resolution 1.58 Å R-free 0.150 |
| 4YUO High-resolution multiconformer synchrotron model of CypA at 273 K Deposited 2015-03-18 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format.
|
Resolution 1.20 Å R-free 0.146 |
| 4YUP Multiconformer fixed-target X-ray free electron (XFEL) model of CypA at 273 K Deposited 2015-03-18 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；Crystals were grown by mixing equal volumes of well solution (100 mM HEPES pH 7.5, 23% PEG 3350, 5 mM TCEP) and protein (60 mg/mL in 20 mM HEPES pH 7.5, 100 mM NaCl, 0.5 mM TCEP) in the hanging-drop format.
|
Resolution 1.75 Å R-free 0.249 |
| 5F66 High-resolution isotropic multiconformer synchrotron model of CypA at 273 K Deposited 2015-12-05 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.15 Å R-free 0.195 |
| 5FJB Cyclophilin A Stabilize HIV-1 Capsid through a Novel Non- canonical Binding Site Deposited 2015-10-07 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain C
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 9.00 Å |
| 5KUL Human cyclophilin A at 100K, Data set 1 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING DROP FORMAT.
|
Resolution 1.70 Å R-free 0.219 |
| 5KUN Human cyclophilin A at 100K, Data set 2 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.208 |
| 5KUO Human cyclophilin A at 100K, Data set 3 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.214 |
| 5KUQ Human cyclophilin A at 100K, Data set 4 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.211 |
| 5KUR Human cyclophilin A at 100K, Data set 5 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.207 |
| 5KUS Human cyclophilin A at 100K, Data set 6 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.213 |
| 5KUU Human cyclophilin A at 100K, Data set 7 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.208 |
| 5KUV Human cyclophilin A at 100K, Data set 8 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.194 |
| 5KUW Human cyclophilin A at 100K, Data set 9 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.213 |
| 5KUZ Human cyclophilin A at 278K, Data set 1 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.184 |
| 5KV0 Human cyclophilin A at 278K, Data set 2 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.193 |
| 5KV1 Human cyclophilin A at 278K, Data set 3 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.198 |
| 5KV2 Human cyclophilin A at 278K, Data set 4 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.203 |
| 5KV3 Human cyclophilin A at 278K, Data set 5 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.201 |
| 5KV4 Human cyclophilin A at 278K, Data set 6 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.200 |
| 5KV5 Human cyclophilin A at 278K, Data set 7 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.210 |
| 5KV6 Human cyclophilin A at 278K, Data set 8 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.224 |
| 5KV7 Human cyclophilin A at 278K, Data set 9 Deposited 2016-07-13 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；CRYSTALS WERE GROWN BY MIXING EQUAL VOLUMES OF WELL SOLUTION (100 MM HEPES PH 7.5, 23% PEG 3350, 5 MM TCEP) AND PROTEIN (60 MG/ML IN 20 MM HEPES PH 7.5, 100 MM NACL, 0.5 MM TCEP) IN THE HANGING-DROP FORMAT.
|
Resolution 1.70 Å R-free 0.223 |
| 5NOQ Structure of cyclophilin A in complex with 3-chloropyridin-2-amine Deposited 2017-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | 93E 3-chloranylpyridin-2-amine × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.60 Å R-free 0.196 |
| 5NOR Structure of cyclophilin A in complex with 3-methylpyridin-2-amine Deposited 2017-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | 93Q 3-methylpyridin-2-amine × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.80 Å R-free 0.203 |
| 5NOS Structure of cyclophilin A in complex with 3-amino-1H-pyridin-2-one Deposited 2017-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | 92Z 5-azanyl-3~{H}-pyridin-6-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.35 Å R-free 0.165 |
| 5NOT Structure of cyclophilin A in complex with 4-chloropyrimidin-5-amine Deposited 2017-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | 938 4-chloranylpyrimidin-5-amine × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.45 Å R-free 0.183 |
| 5NOU Structure of cyclophilin A in complex with hexahydropyrimidin-2-one Deposited 2017-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | L60 1,3-diazinan-2-one × 3 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.30 Å R-free 0.163 |
| 5NOV Structure of cyclophilin A in complex with hexahydropyrimidine-2-thione Deposited 2017-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | 93B 1,3-diazinane-2-thione × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 2.00 Å R-free 0.265 |
| 5NOW Structure of cyclophilin A in complex with pyridine-3,4-diamine Deposited 2017-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | L89 pyridine-3,4-diamine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.48 Å R-free 0.219 |
| 5NOX Structure of cyclophilin A in complex with 2-chloropyridin-3-amine Deposited 2017-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | L97 2-chloranylpyridin-3-amine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.49 Å R-free 0.199 |
| 5NOY Structure of cyclophilin A in complex with 3,4-diaminobenzamide Deposited 2017-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | 93K 3,4-bis(azanyl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.43 Å R-free 0.182 |
| 5NOZ Structure of cyclophilin A in complex with 3,4-diaminobenzohydrazide Deposited 2017-04-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | L99 3,4-bis(azanyl)benzohydrazide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.61 Å R-free 0.216 |
| 5T9U Discovery of a Potent Cyclophilin Inhibitor (Compound 3) based on Structural Simplification of Sanglifehrin A Deposited 2016-09-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–164（164 aa）
|
Not recorded | 7HG 3-[(3-hydroxyphenyl)methyl]-10,12-dimethoxy-9,11-dimethyl-6-(propan-2-yl)-19-oxa-1,4,7,25-tetraazabicyclo[19.3.1]pentacosa-13,15-diene-2,5,8,20-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；293 K；0.1 M Tris-HCl, pH 8.5
0.1 M potassium chloride
2.2 M ammonium sulfate
|
Resolution 2.30 Å R-free 0.193 |
| 5T9U Discovery of a Potent Cyclophilin Inhibitor (Compound 3) based on Structural Simplification of Sanglifehrin A Deposited 2016-09-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–164（164 aa）
|
Not recorded | 7HG 3-[(3-hydroxyphenyl)methyl]-10,12-dimethoxy-9,11-dimethyl-6-(propan-2-yl)-19-oxa-1,4,7,25-tetraazabicyclo[19.3.1]pentacosa-13,15-diene-2,5,8,20-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；293 K；0.1 M Tris-HCl, pH 8.5
0.1 M potassium chloride
2.2 M ammonium sulfate
|
Resolution 2.30 Å R-free 0.193 |
| 5T9U Discovery of a Potent Cyclophilin Inhibitor (Compound 3) based on Structural Simplification of Sanglifehrin A Deposited 2016-09-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–164（164 aa）
|
Not recorded | 7HG 3-[(3-hydroxyphenyl)methyl]-10,12-dimethoxy-9,11-dimethyl-6-(propan-2-yl)-19-oxa-1,4,7,25-tetraazabicyclo[19.3.1]pentacosa-13,15-diene-2,5,8,20-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；293 K；0.1 M Tris-HCl, pH 8.5
0.1 M potassium chloride
2.2 M ammonium sulfate
|
Resolution 2.30 Å R-free 0.193 |
| 5T9U Discovery of a Potent Cyclophilin Inhibitor (Compound 3) based on Structural Simplification of Sanglifehrin A Deposited 2016-09-09 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–164（164 aa）
|
Not recorded | 7HG 3-[(3-hydroxyphenyl)methyl]-10,12-dimethoxy-9,11-dimethyl-6-(propan-2-yl)-19-oxa-1,4,7,25-tetraazabicyclo[19.3.1]pentacosa-13,15-diene-2,5,8,20-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；293 K；0.1 M Tris-HCl, pH 8.5
0.1 M potassium chloride
2.2 M ammonium sulfate
|
Resolution 2.30 Å R-free 0.193 |
| 5T9W Discovery of a Potent Cyclophilin Inhibitor (Compound 5) based on Structural Simplification of Sanglifehrin A Deposited 2016-09-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | 78E 3-[(3-hydroxyphenyl)methyl]-6-(propan-2-yl)-19-oxa-1,4,7,25-tetraazabicyclo[19.3.1]pentacosa-13,15-diene-2,5,8,20-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；0.05 M monobasic potassium phosphate
20% (w/v) PEG 8000
|
Resolution 2.00 Å R-free 0.184 |
| 5T9Z Discovery of a Potent Cyclophilin Inhibitor (Compound 6) based on Structural Simplification of Sanglifehrin A Deposited 2016-09-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–164（163 aa）
|
Not recorded | 78R 11-[(3-hydroxyphenyl)methyl]-18-methoxy-17-methyl-14-(propan-2-yl)-3-oxa-9,12,15,28-tetraazatricyclo[21.3.1.1~5,9~]octacosa-1(27),21,23,25-tetraene-4,10,13,16-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 4.2；293 K；sodium citrate, pH 4.2
25% (w/v) PEG 3350
|
Resolution 1.40 Å R-free 0.190 |
| 5TA2 Discovery of a Potent Cyclophilin Inhibitor (Compound 7) based on Structural Simplification of Sanglifehrin A Deposited 2016-09-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–164（163 aa）
|
Not recorded | 78X 11-[(3-hydroxyphenyl)methyl]-18-methoxy-2,17-dimethyl-14-(propan-2-yl)-3-oxa-9,12,15,28-tetraazatricyclo[21.3.1.1~5,9~]octacosa-1(27),21,23,25-tetraene-4,10,13,16-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；sodium citrate, pH 4.2
25% (w/v) PEG 3350
|
Resolution 1.48 Å R-free 0.183 |
| 5TA4 Discovery of a Potent Cyclophilin Inhibitor (Compound 8) based on Structural Simplification of Sanglifehrin A Deposited 2016-09-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–165（164 aa）
|
Not recorded | 838 18-methoxy-2,11,17-trimethyl-14-(propan-2-yl)-3-oxa-9,12,15,28-tetraazatricyclo[21.3.1.1~5,9~]octacosa-1(27),21,23,25-tetraene-4,10,13,16-tetrone × 1 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 8.5；293 K；0.1 M Tris-HCl, pH 8.5
0.2 M potassium chloride
2.0 M ammonium sulfate
|
Resolution 1.50 Å R-free 0.206 |
| 5WC7 CypA Mutant - I97V S99T C115S Deposited 2017-06-29 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Mutation：I97V, S99T, C115S | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100 MM HEPES PH 7.5, 22% PEG 3350
|
Resolution 1.43 Å R-free 0.127 |
| 6BTA CypA Mutant - S99T C115S Deposited 2017-12-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Mutation：S99T, C115S | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；100 MM HEPES PH 7.5, 22% PEG 3350
|
Resolution 1.50 Å R-free 0.146 |
| 6GJI Cyclophilin A complexed with the tri-vector ligand 8. Deposited 2018-05-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | F1E ethyl 2-[[(4-aminophenyl)methyl-[(1-methyl-1,2,3-triazol-4-yl)methyl]carbamoyl]amino]ethanoate × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.60 Å R-free 0.191 |
| 6GJJ Cyclophilin A complexed with tri-vector ligand 2. Deposited 2018-05-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | L36 ethyl 2-[[(4-aminophenyl)methyl-propyl-carbamoyl]amino]ethanoate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.38 Å R-free 0.185 |
| 6GJL Cyclophilin A complexed with tri-vector ligand 10. Deposited 2018-05-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | F1Q ethyl 2-[[(4-aminophenyl)methyl-(1~{H}-1,2,3,4-tetrazol-5-ylmethyl)carbamoyl]amino]ethanoate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.16 Å R-free 0.192 |
| 6GJM Cyclophilin A complexed with tri-vector ligand 4. Deposited 2018-05-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | L36 ethyl 2-[[(4-aminophenyl)methyl-propyl-carbamoyl]amino]ethanoate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.35 Å R-free 0.178 |
| 6GJN Cyclophilin A complexed with tri-vector ligand 15. Deposited 2018-05-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | F0Q 1-[(4-aminophenyl)methyl]-3-[2-[(2~{R})-2-(2-bromophenyl)pyrrolidin-1-yl]-2-oxidanylidene-ethyl]-1-[(2-methyl-1,2,3,4-tetrazol-5-yl)methyl]urea × 1 FMT FORMIC ACID × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.70 Å R-free 0.203 |
| 6GJP Cyclophilin A complexed with tri-vector ligand 7. Deposited 2018-05-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | F0T ethyl 2-[[(4-aminophenyl)methyl-(cyclopropylmethyl)carbamoyl]amino]ethanoate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.94 Å R-free 0.237 |
| 6GJR Cyclophilin A complexed with tri-vector ligand 9. Deposited 2018-05-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | F0W ethyl 2-[[(4-aminophenyl)methyl-[(2-methyl-1,2,3,4-tetrazol-5-yl)methyl]carbamoyl]amino]ethanoate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.69 Å R-free 0.262 |
| 6GJY Cyclophilin A complexed with tri-vector ligand 5. Deposited 2018-05-17 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | F1Z ethyl 2-[[(4-aminophenyl)methyl-prop-2-ynyl-carbamoyl]amino]ethanoate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；279.15 K；PEG 8000, Tris-HCl
|
Resolution 1.29 Å R-free 0.188 |
| 6GS6 Cyclophilin A single mutant D66A in complex with an inhibitor. Deposited 2018-06-13 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Mutation：D66A | EA4 ethyl N-[(4-aminobenzyl)carbamoyl]glycinate × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289.15 K；2.2 M Ammonium Sulfate
|
Resolution 1.16 Å R-free 0.170 |
| 6I42 Structure of the alpha-Synuclein PreNAC/Cyclophilin A-complex Deposited 2018-11-08 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7；293 K；1.93 M tri-ammonium citrate, pH 7.0
|
Resolution 1.38 Å R-free 0.178 |
| 6U5C RT XFEL structure of CypA solved using MESH injection system Deposited 2019-08-27 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.5；291 K；100 mM HEPES, pH 7.5, 5 mM TCEP, 20% PEG3350
|
Resolution 1.62 Å R-free 0.157 |
| 6U5D RT XFEL structure of CypA solved using LCP injection system Deposited 2019-08-27 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.5；291 K；100 mM HEPES, pH 7.5, 5 mM TCEP, 20% PEG3350
|
Resolution 1.65 Å R-free 0.167 |
| 6U5E RT XFEL structure of CypA solved using celloluse carrier media Deposited 2019-08-27 | Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
BATCH MODE；pH 7.5；291 K；100 mM HEPES, pH 7.5, 5 mM TCEP, 20% PEG3350
|
Resolution 1.56 Å R-free 0.151 |
| 6U5G MicroED structure of a FIB-milled CypA Crystal Deposited 2019-08-27 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON CRYSTALLOGRAPHY
cryo-EM buffer
pH 7.5
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 2.50 Å R-free 0.224 |
| 6X3R Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors Deposited 2020-05-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | ZXX methyl (3~{S})-1-[(2~{S})-2-[[(2~{S})-2-acetamido-3-methyl-butanoyl]amino]-3-(3-hydroxyphenyl)propanoyl]-1,2-diazinane-3-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20 mM Tris-HCl, pH 8.5, 2 mM DTT, 2 mM EDTA, 20-35% PEG3350, 5% ethanol
|
Resolution 1.80 Å R-free 0.197 |
| 6X3Y Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors Deposited 2020-05-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | UMM tert-butyl [(2S)-1-{[(3S,17S)-2,16-dioxo-10,15-dioxa-1,21-diazatricyclo[15.3.1.1~5,9~]docosa-5(22),6,8-trien-3-yl]amino}-3-methyl-1-oxobutan-2-yl]carbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20 mM Tris-HCl, pH 8.5, 2 mM DTT, 2 mM EDTA, 20-35% PEG3350, 5% ethanol
|
Resolution 1.40 Å R-free 0.171 |
| 6X4M Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors: tert-butyl [(2S)-1-{[(3S,17S)-2,16-dioxo-10,15-dioxa-1,21-diazatricyclo[15.3.1.1~5,9~]docosa-5(22),6,8-trien-3-yl]amino}-3-methyl-1-oxobutan-2-yl]carbamate (compound 3) Deposited 2020-05-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | UMM tert-butyl [(2S)-1-{[(3S,17S)-2,16-dioxo-10,15-dioxa-1,21-diazatricyclo[15.3.1.1~5,9~]docosa-5(22),6,8-trien-3-yl]amino}-3-methyl-1-oxobutan-2-yl]carbamate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20 mM Tris-HCl, pH 8.5, 2 mM DTT, 2 mM EDTA, 20-35% PEG3350, 5% ethanol
|
Resolution 1.50 Å R-free 0.171 |
| 6X4N Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors: (2R,5S,11S,14S,18E)-2,11,17,17-tetramethyl-14-(propan-2-yl)-3-oxa-9,12,15,26,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(25),18,20(28),21,23,26-hexaene-4,10,13,16-tetrone (compound 24) Deposited 2020-05-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | UOD (2R,5S,11S,14S,18E)-2,11,17,17-tetramethyl-14-(propan-2-yl)-3-oxa-9,12,15,26,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(25),18,20(28),21,23,26-hexaene-4,10,13,16-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20 mM Tris-HCl, pH 8.5, 2 mM DTT, 2 mM EDTA, 20-35% PEG3350, 5% ethanol
|
Resolution 1.51 Å R-free 0.180 |
| 6X4O Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors: (2R,5S,11S,14S,18E)-2,11-dimethyl-14-(propan-2-yl)-3-oxa-9,12,15,21,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(26),18,20,22,24,27-hexaene-4,10,13,16-tetrone (compound 21) Deposited 2020-05-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | UO7 (2R,5S,11S,14S,18E)-2,11-dimethyl-14-(propan-2-yl)-3-oxa-9,12,15,21,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(26),18,20,22,24,27-hexaene-4,10,13,16-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20 mM Tris-HCl, pH 8.5, 2 mM DTT, 2 mM EDTA, 20-35% PEG3350, 5% ethanol
|
Resolution 1.50 Å R-free 0.198 |
| 6X4P Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors: (2R,5S,11S,14S,18E)-2,11,17,17-tetramethyl-14-(propan-2-yl)-15-oxa-3,9,12,26,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(25),18,20(28),21,23,26-hexaene-4,10,13,16-tetrone (compound 28) Deposited 2020-05-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | UOG (2R,5S,11S,14S,18E)-2,11,17,17-tetramethyl-14-(propan-2-yl)-15-oxa-3,9,12,26,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(25),18,20(28),21,23,26-hexaene-4,10,13,16-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；277 K；20 mM Tris-HCl, pH 8.5, 2 mM DTT, 2 mM EDTA, 20-35% PEG3350, 5% ethanol
|
Resolution 1.50 Å R-free 0.177 |
| 6X4Q Human cyclophilin A bound to a series of acylcic and macrocyclic inhibitors: (2R,5S,11S,14S,18E)-14-cyclobutyl-2,11,17,17-tetramethyl-15-oxa-3,9,12,26,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(25),18,20(28),21,23,26-hexaene-4,10,13,16-tetrone (compound 33) Deposited 2020-05-22 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | UOJ (2R,5S,11S,14S,18E)-14-cyclobutyl-2,11,17,17-tetramethyl-15-oxa-3,9,12,26,29-pentaazatetracyclo[18.5.3.1~5,9~.0~23,27~]nonacosa-1(25),18,20(28),21,23,26-hexaene-4,10,13,16-tetrone × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20 mM Tris-HCl, pH 8.5, 2 mM DTT, 2 mM EDTA, 20-35% PEG 3350, 5% ethanol
|
Resolution 1.80 Å R-free 0.191 |
| 6Y9V Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-8,13) Deposited 2020-03-10 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain J
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.90 Å |
| 6Y9W Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,8) Deposited 2020-03-10 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain J
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.10 Å |
| 6Y9X Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,7) Deposited 2020-03-10 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain J
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.40 Å |
| 6Y9Y Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-7,13) Deposited 2020-03-10 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain J
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 6.10 Å |
| 6Y9Z Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,9) Deposited 2020-03-10 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain J
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 4.80 Å |
| 6ZDJ Structure of the native full-length HIV-1 capsid protein in complex with Cyclophilin A from helical assembly (-13,10) Deposited 2020-06-14 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 13 PDB declaration: tridecameric |
Chain J
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.80 Å |
| 7ABT Structure of PPIA in complex with PR dipeptide repeat Deposited 2020-09-08 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–164（163 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；293 K；0.1 M HEPES, 25% PEG1000
|
Resolution 1.31 Å R-free 0.166 |
| 7N9X CA-targeting nanobody is a tool for studying HIV-1 capsid lattice interactions Deposited 2021-06-18 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 18 PDB declaration: octadecameric |
Chain GGG
1–165（165 aa）
Chain HHH
1–165（165 aa）
Chain III
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；295 K；100 mM Bis-Tris propane, pH 6.8, 15% PEG3350, 200 mM sodium
|
Resolution 3.51 Å R-free 0.270 |
| 7PCJ X-ray structure of CypA-C52AK125C/CsA/aromatic foldamer complex Deposited 2021-08-03 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–165（165 aa）
|
Mutation：K125C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；Tris 0.1M, PEG 3350 15%, NaN3 3mM
|
Resolution 1.91 Å R-free 0.219 |
| 7PCJ X-ray structure of CypA-C52AK125C/CsA/aromatic foldamer complex Deposited 2021-08-03 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain D
1–165（165 aa）
|
Mutation：K125C | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.4；293 K；Tris 0.1M, PEG 3350 15%, NaN3 3mM
|
Resolution 1.91 Å R-free 0.219 |
| 7QBW Human Cyclophilin A double mutant C52AK125C Deposited 2021-11-19 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；HEPES 60mM, NaCl 50mM, TCEP 5mM, 10% PEG 3350, NaN3 1.5mM
|
Resolution 1.59 Å R-free 0.191 |
| 7TA8 NMR structure of crosslinked cyclophilin A Deposited 2021-12-20 | Different construct Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 25；Pressure 1
NMR sample composition
390 uM [U-13C; U-15N] cyclophilin A, 93% H2O/7% D2O | 93% H2O/7% D2O
|
Resolution not provided |
| 7UPN Maedi visna virus Vif in complex with CypA and E3 ubiquitin ligase Deposited 2022-04-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–165（165 aa）
Chain B
1–165（165 aa）
|
Not recorded | ZN ZINC ION × 2 |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 7.2
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 3.50 Å |
| 7UXJ Structure of PPIA in complex with FP29102, a Helicon Polypeptide Deposited 2022-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–165（165 aa）
|
Not recorded | NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 2.07 Å R-free 0.262 |
| 7UXJ Structure of PPIA in complex with FP29102, a Helicon Polypeptide Deposited 2022-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–165（165 aa）
|
Not recorded | NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 2.07 Å R-free 0.262 |
| 7UXJ Structure of PPIA in complex with FP29102, a Helicon Polypeptide Deposited 2022-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 2.07 Å R-free 0.262 |
| 7UXJ Structure of PPIA in complex with FP29102, a Helicon Polypeptide Deposited 2022-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 2.07 Å R-free 0.262 |
| 7UXM Structure of PPIA in complex with FP29092, a Helicon Polypeptide Deposited 2022-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–165（165 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 1.20 Å R-free 0.190 |
| 7UXM Structure of PPIA in complex with FP29092, a Helicon Polypeptide Deposited 2022-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–165（165 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 5 NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 1.20 Å R-free 0.190 |
| 7UXM Structure of PPIA in complex with FP29092, a Helicon Polypeptide Deposited 2022-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | EDO 1,2-ETHANEDIOL × 6 NH2 AMINO GROUP × 1 WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.15 M Potassium bromide, 30% w/v Polyethylene glycol monomethyl ether 2,000
|
Resolution 1.20 Å R-free 0.190 |
| 7UXN Structure of PPIA in complex with FP29103, a Helicon Polypeptide Deposited 2022-05-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–165（165 aa）
|
Not recorded | WHL N,N'-(1,4-phenylene)diacetamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；0.2 M Sodium acetate, 0.1 M Sodium cacodylate pH 6.5, 30% w/v PEG 8000.
|
Resolution 1.36 Å R-free 0.217 |
| 8G9P Tricomplex of RMC-4998, KRAS G12C, and CypA Deposited 2023-02-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 YV2 (2S)-2-{(5S)-7-[(2E)-4-(dimethylamino)-4-methylpent-2-enoyl]-1-oxo-2,7-diazaspiro[4.4]nonan-2-yl}-N-[(1P,8S,10R,14S,21M)-22-ethyl-21-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]-3-methylbutanamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；22% PEG 3350, 100 mM NaCl
|
Resolution 1.50 Å R-free 0.188 |
| 8G9P Tricomplex of RMC-4998, KRAS G12C, and CypA Deposited 2023-02-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 YV2 (2S)-2-{(5S)-7-[(2E)-4-(dimethylamino)-4-methylpent-2-enoyl]-1-oxo-2,7-diazaspiro[4.4]nonan-2-yl}-N-[(1P,8S,10R,14S,21M)-22-ethyl-21-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]-3-methylbutanamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；22% PEG 3350, 100 mM NaCl
|
Resolution 1.50 Å R-free 0.188 |
| 8G9Q Tricomplex of Compound-1, KRAS G12C, and CypA Deposited 2023-02-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 YV6 methyl (3S)-1-[N-(4-sulfanylbutanoyl)-L-valyl-3-hydroxy-L-phenylalanyl]-1,2-diazinane-3-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；22% PEG 3350, 100 mM NaCl, 100 mM Bis-Tris pH 5.5
|
Resolution 1.40 Å R-free 0.214 |
| 8HZ8 Structure of PPIA in complex with the peptide of NRF2 Deposited 2023-01-08 | Different construct Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–165（164 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, Hepes, TCEP
|
Resolution 1.81 Å R-free 0.248 |
| 8TBF Tricomplex of RMC-7977, KRAS WT, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；24% PEG4000, 0.1 M Tris-HCl, pH 8.0
|
Resolution 1.50 Å R-free 0.210 |
| 8TBF Tricomplex of RMC-7977, KRAS WT, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；24% PEG4000, 0.1 M Tris-HCl, pH 8.0
|
Resolution 1.50 Å R-free 0.210 |
| 8TBG Tricomplex of RMC-7977, HRAS WT, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；28% PEG4000, 0.1 M Tris, pH 8
|
Resolution 1.20 Å R-free 0.192 |
| 8TBG Tricomplex of RMC-7977, HRAS WT, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；28% PEG4000, 0.1 M Tris, pH 8
|
Resolution 1.20 Å R-free 0.192 |
| 8TBH Tricomplex of RMC-7977, KRAS G12R, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；17% PEG4000, 0.1 M imidazole, pH 8.0
|
Resolution 1.50 Å R-free 0.225 |
| 8TBH Tricomplex of RMC-7977, KRAS G12R, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；17% PEG4000, 0.1 M imidazole, pH 8.0
|
Resolution 1.50 Å R-free 0.225 |
| 8TBI Tricomplex of RMC-7977, NRAS WT, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；27% PEG4000, 0.1 M Tris-HCl, pH 8.0
|
Resolution 1.59 Å R-free 0.208 |
| 8TBI Tricomplex of RMC-7977, NRAS WT, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；27% PEG4000, 0.1 M Tris-HCl, pH 8.0
|
Resolution 1.59 Å R-free 0.208 |
| 8TBJ Tricomplex of RMC-7977, KRAS G12A, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；24% PEG4000, 0.1 M Tris-HCl, pH 8.0
|
Resolution 1.45 Å R-free 0.215 |
| 8TBJ Tricomplex of RMC-7977, KRAS G12A, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；24% PEG4000, 0.1 M Tris-HCl, pH 8.0
|
Resolution 1.45 Å R-free 0.215 |
| 8TBK Tricomplex of RMC-7977, KRAS G12C, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；27% PEG4000, 0.1 M imidazole, pH 7.0
|
Resolution 1.26 Å R-free 0.184 |
| 8TBK Tricomplex of RMC-7977, KRAS G12C, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；27% PEG4000, 0.1 M imidazole, pH 7.0
|
Resolution 1.26 Å R-free 0.184 |
| 8TBL Tricomplex of RMC-7977, KRAS G12D, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；25% PEG4000, 0.1 M Tris-HCl, pH 8.0
|
Resolution 1.88 Å R-free 0.227 |
| 8TBL Tricomplex of RMC-7977, KRAS G12D, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；25% PEG4000, 0.1 M Tris-HCl, pH 8.0
|
Resolution 1.88 Å R-free 0.227 |
| 8TBM Tricomplex of RMC-7977, KRAS G12V, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；24% PEG6000, 0.1 M imidazole, pH 7
|
Resolution 1.57 Å R-free 0.211 |
| 8TBM Tricomplex of RMC-7977, KRAS G12V, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 GOL GLYCEROL × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；24% PEG6000, 0.1 M imidazole, pH 7
|
Resolution 1.57 Å R-free 0.211 |
| 8TBN Tricomplex of RMC-7977, KRAS G12S, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；22% PEG6000, 0.1 M imidazole, pH 7
|
Resolution 1.46 Å R-free 0.197 |
| 8TBN Tricomplex of RMC-7977, KRAS G12S, and CypA Deposited 2023-06-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；22% PEG6000, 0.1 M imidazole, pH 7
|
Resolution 1.46 Å R-free 0.197 |
| 9AX6 Tricomplex of RMC-6236, KRAS G12D, and CypA Deposited 2024-03-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris, pH 8.0, 25% PEG4000
|
Resolution 1.65 Å R-free 0.227 |
| 9AX6 Tricomplex of RMC-6236, KRAS G12D, and CypA Deposited 2024-03-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M Tris, pH 8.0, 25% PEG4000
|
Resolution 1.65 Å R-free 0.227 |
| 9BFV Tri-complex of Compound-23, KRAS G12C, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 A1AOV (3R)-1-[(2E)-4-(dimethylamino)-4-methylpent-2-enoyl]-N-[(2S)-1-{[(1P,8R,10R,14S,21M)-22-ethyl-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-N-methylpyrrolidine-3-carboxamide (non-preferred name) × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl
|
Resolution 1.20 Å R-free 0.189 |
| 9BFV Tri-complex of Compound-23, KRAS G12C, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 A1AOV (3R)-1-[(2E)-4-(dimethylamino)-4-methylpent-2-enoyl]-N-[(2S)-1-{[(1P,8R,10R,14S,21M)-22-ethyl-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-N-methylpyrrolidine-3-carboxamide (non-preferred name) × 1 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl
|
Resolution 1.20 Å R-free 0.189 |
| 9BFW Tri-complex of Compound-4, KRAS G12C, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 A1AOM 1-acetyl-N-[(2S)-1-{[(1M,8S,10R,14S,20S)-22-cyano-4-hydroxy-18,18-dimethyl-9,15-dioxo-16-oxa-10,20,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,21,23,26-heptaen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-N-methylazetidine-3-carboxamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 3350, 0.1M Bis Tris, pH 5.5
|
Resolution 1.20 Å R-free 0.147 |
| 9BFX Tri-complex of Elironrasib (RMC-6291), KRAS G12C, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AOD 1-[(2E)-4-(dimethylamino)-4-methylpent-2-enoyl]-N-[(2R)-1-{[(2S,6S,8S,10R,14S,21M)-22-ethyl-21-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-5,16-dioxa-2,10,22,28-tetraazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),20,23,26-tetraen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-4-fluoro-N-methylpiperidine-4-carboxamide (non-preferred name) × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG3350, 0.1 M Bis-Tris, pH 5.5, 150 mM sodium chloride
|
Resolution 1.40 Å R-free 0.209 |
| 9BFX Tri-complex of Elironrasib (RMC-6291), KRAS G12C, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AOD 1-[(2E)-4-(dimethylamino)-4-methylpent-2-enoyl]-N-[(2R)-1-{[(2S,6S,8S,10R,14S,21M)-22-ethyl-21-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-5,16-dioxa-2,10,22,28-tetraazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),20,23,26-tetraen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-4-fluoro-N-methylpiperidine-4-carboxamide (non-preferred name) × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG3350, 0.1 M Bis-Tris, pH 5.5, 150 mM sodium chloride
|
Resolution 1.40 Å R-free 0.209 |
| 9BFY Tri-complex of Compound-14, KRAS G12C, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 A1AOL (3R)-N-[(2S)-1-{[(1M,8R,10R,14S,21M)-22-ethyl-4-hydroxy-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-N-methyl-1-propanoylpyrrolidine-3-carboxamide (non-preferred name) × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl
|
Resolution 1.26 Å R-free 0.189 |
| 9BFY Tri-complex of Compound-14, KRAS G12C, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 A1AOL (3R)-N-[(2S)-1-{[(1M,8R,10R,14S,21M)-22-ethyl-4-hydroxy-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-N-methyl-1-propanoylpyrrolidine-3-carboxamide (non-preferred name) × 1 CL CHLORIDE ION × 1 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl
|
Resolution 1.26 Å R-free 0.189 |
| 9BFZ Tri-complex of Compound-5, KRAS G12C, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AOK (3R)-N-[(2S)-1-{[(1M,8R,10S,14S,21M)-22-ethyl-4-hydroxy-21-[2-(2-methoxyethyl)phenyl]-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-N-methyl-1-propanoylpyrrolidine-3-carboxamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 3350, 0.1M Bis-Tris, pH 5.5, 150 mM NaCl
|
Resolution 1.80 Å R-free 0.222 |
| 9BFZ Tri-complex of Compound-5, KRAS G12C, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AOK (3R)-N-[(2S)-1-{[(1M,8R,10S,14S,21M)-22-ethyl-4-hydroxy-21-[2-(2-methoxyethyl)phenyl]-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-N-methyl-1-propanoylpyrrolidine-3-carboxamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；25% PEG 3350, 0.1M Bis-Tris, pH 5.5, 150 mM NaCl
|
Resolution 1.80 Å R-free 0.222 |
| 9BG0 Tri-complex of Daraxonrasib (RMC-6236), NRAS WT, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；29% PEG4000, 0.1 M Tris, pH 8
|
Resolution 1.64 Å R-free 0.236 |
| 9BG0 Tri-complex of Daraxonrasib (RMC-6236), NRAS WT, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；29% PEG4000, 0.1 M Tris, pH 8
|
Resolution 1.64 Å R-free 0.236 |
| 9BG1 Tri-complex of Compound-3, KRAS G12V, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AOH (2R)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-methyl-2-(N-methylacetamido)butanamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；28% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl
|
Resolution 1.51 Å R-free 0.226 |
| 9BG1 Tri-complex of Compound-3, KRAS G12V, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AOH (2R)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-methyl-2-(N-methylacetamido)butanamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；28% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl
|
Resolution 1.51 Å R-free 0.226 |
| 9BG2 Tri-complex of Compound-10, KRAS G12V, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AOJ (1S,2R)-N-[(1P,7S,9S,13S,20M)-21-ethyl-20-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；28% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl
|
Resolution 1.64 Å R-free 0.228 |
| 9BG2 Tri-complex of Compound-10, KRAS G12V, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AOJ (1S,2R)-N-[(1P,7S,9S,13S,20M)-21-ethyl-20-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；28% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl
|
Resolution 1.64 Å R-free 0.228 |
| 9BG3 Tri-complex of Daraxonrasib (RMC-6236), NRAS Q61K, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；25.5% PEG4000, 0.1 M Tris, pH 8
|
Resolution 1.33 Å R-free 0.198 |
| 9BG3 Tri-complex of Daraxonrasib (RMC-6236), NRAS Q61K, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；25.5% PEG4000, 0.1 M Tris, pH 8
|
Resolution 1.33 Å R-free 0.198 |
| 9BG4 Tri-complex of Compound-2, KRAS G12V, and CypA Deposited 2024-04-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: dimeric |
Chain C
1–165（165 aa）
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 2 A1AOG (2R)-N-[(1P,8S,10S,14S,21M)-22-ethyl-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]-3-methyl-2-(N-methylacetamido)butanamide (non-preferred name) × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；28% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 nM NaCl
|
Resolution 1.14 Å R-free 0.177 |
| 9BG4 Tri-complex of Compound-2, KRAS G12V, and CypA Deposited 2024-04-18 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: dimeric |
Chain C
1–165（165 aa）
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 CL CHLORIDE ION × 2 A1AOG (2R)-N-[(1P,8S,10S,14S,21M)-22-ethyl-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]-3-methyl-2-(N-methylacetamido)butanamide (non-preferred name) × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；28% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 nM NaCl
|
Resolution 1.14 Å R-free 0.177 |
| 9BG5 Tri-complex of Daraxonrasib (RMC-6236), KRAS G13D, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；24% PEG4000, 0.1 M imidazole, pH 7
|
Resolution 1.67 Å R-free 0.266 |
| 9BG5 Tri-complex of Daraxonrasib (RMC-6236), KRAS G13D, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；24% PEG4000, 0.1 M imidazole, pH 7
|
Resolution 1.67 Å R-free 0.266 |
| 9BG6 Tri-complex of Daraxonrasib (RMC-6236), KRAS G12V, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；25% PEG6000, 0.1 M imidazole, pH 7
|
Resolution 1.66 Å R-free 0.240 |
| 9BG6 Tri-complex of Daraxonrasib (RMC-6236), KRAS G12V, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；25% PEG6000, 0.1 M imidazole, pH 7
|
Resolution 1.66 Å R-free 0.240 |
| 9BG7 Tri-complex of Compound-6, KRAS G12V, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AOI N-[(2R)-1-{[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]amino}-3-methyl-1-oxobutan-2-yl]-3-methoxy-N-methylazetidine-1-carboxamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；28% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl
|
Resolution 1.60 Å R-free 0.203 |
| 9BG7 Tri-complex of Compound-6, KRAS G12V, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AOI N-[(2R)-1-{[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]amino}-3-methyl-1-oxobutan-2-yl]-3-methoxy-N-methylazetidine-1-carboxamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；28% PEG 3350, 0.1M Bis Tris, pH 5.5, 150 mM NaCl
|
Resolution 1.60 Å R-free 0.203 |
| 9BG8 Tri-complex of Daraxonrasib (RMC-6236), NRAS Q61R, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% PEG3350, 0.1 M Bis-Tris, pH 5.5, 150 mM sodium chloride
|
Resolution 1.20 Å R-free 0.186 |
| 9BG8 Tri-complex of Daraxonrasib (RMC-6236), NRAS Q61R, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；25% PEG3350, 0.1 M Bis-Tris, pH 5.5, 150 mM sodium chloride
|
Resolution 1.20 Å R-free 0.186 |
| 9BG9 Tri-complex of Daraxonrasib (RMC-6236), KRAS WT, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；25% PEG6000, 0.1 M imidazole, pH 7
|
Resolution 1.58 Å R-free 0.231 |
| 9BG9 Tri-complex of Daraxonrasib (RMC-6236), KRAS WT, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；291 K；25% PEG6000, 0.1 M imidazole, pH 7
|
Resolution 1.58 Å R-free 0.231 |
| 9BGA Tri-complex of Daraxonrasib (RMC-6236), KRAS G12C, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；28% PEG4000, 0.1 M Tris, pH 8
|
Resolution 1.41 Å R-free 0.229 |
| 9BGA Tri-complex of Daraxonrasib (RMC-6236), KRAS G12C, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；28% PEG4000, 0.1 M Tris, pH 8
|
Resolution 1.41 Å R-free 0.229 |
| 9BGB Tri-complex of Daraxonrasib (RMC-6236), KRAS Q61H, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；29% PEG4000, 0.1 M Tris, pH 8
|
Resolution 1.68 Å R-free 0.230 |
| 9BGB Tri-complex of Daraxonrasib (RMC-6236), KRAS Q61H, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 8；291 K；29% PEG4000, 0.1 M Tris, pH 8
|
Resolution 1.68 Å R-free 0.230 |
| 9BGC Tri-complex of Daraxonrasib (RMC-6236), KRAS G12R, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；22% PEG2000 MME, 0.10 M Tris, pH 8
|
Resolution 1.87 Å R-free 0.272 |
| 9BGC Tri-complex of Daraxonrasib (RMC-6236), KRAS G12R, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；22% PEG2000 MME, 0.10 M Tris, pH 8
|
Resolution 1.87 Å R-free 0.272 |
| 9BGD Tri-complex of Daraxonrasib (RMC-6236), NRAS Q61L, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；21% PEG3350, 0.1 M Bis-Tris, pH 5.5, 133 mM sodium chloride
|
Resolution 1.76 Å R-free 0.237 |
| 9BGD Tri-complex of Daraxonrasib (RMC-6236), NRAS Q61L, and CypA Deposited 2024-04-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AHB (1R,2S)-N-[(1P,7S,9S,13R,20M)-21-ethyl-20-{2-[(1R)-1-methoxyethyl]-5-(4-methylpiperazin-1-yl)pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-2-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；291 K；21% PEG3350, 0.1 M Bis-Tris, pH 5.5, 133 mM sodium chloride
|
Resolution 1.76 Å R-free 0.237 |
| 9BHO Crystal structure of KRAS G12S in a transition state mimetic complex with CYPA and RMC-7977 Deposited 2024-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–165（165 aa）
Chain D
1–165（165 aa）
|
Not recorded | ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 2 AF3 ALUMINUM FLUORIDE × 2 MG MAGNESIUM ION × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；100 mM Tris pH 8.5, 15% PEG 20000
|
Resolution 1.89 Å R-free 0.218 |
| 9BHP Crystal structure of KRAS G12C in a transition state mimetic complex with CYPA and RMC-7977 Deposited 2024-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–165（165 aa）
Chain D
1–165（165 aa）
|
Not recorded | ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 2 AF3 ALUMINUM FLUORIDE × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；100 mM Tris-HCl pH 8.5, 20% PEG 10000
|
Resolution 2.10 Å R-free 0.253 |
| 9BHQ Crystal structure of KRAS G12A in a transition state mimetic complex with CYPA and RMC-7977 Deposited 2024-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–165（165 aa）
Chain D
1–165（165 aa）
|
Not recorded | ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 2 GDP GUANOSINE-5'-DIPHOSPHATE × 2 AF3 ALUMINUM FLUORIDE × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；100 mM Tris pH 8.5, 15% PEG 10000
|
Resolution 1.90 Å R-free 0.232 |
| 9BI1 Crystal structure of GMPPNP bound KRAS G12D in complex with CYPA and RMC-7977 Deposited 2024-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–165（165 aa）
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；100 mM Tris-HCl pH 8.5, 24% PEG 10000
|
Resolution 1.65 Å R-free 0.260 |
| 9BI2 Crystal structure of GMPPNP bound KRAS G12C in complex with CYPA and RMC-7977 Deposited 2024-04-22 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
1–165（165 aa）
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 2 MG MAGNESIUM ION × 2 ZNI (1R,5S,6r)-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1S)-1-methoxyethyl]pyridin-3-yl}-21-ethyl-17,17-dimethyl-8,14-dioxo-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-oxabicyclo[3.1.0]hexane-6-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291.15 K；100 mM Tris-HCl pH 8.5, 24% PEG 10000
|
Resolution 2.15 Å R-free 0.236 |
| 9CT7 Tricomplex of Compound 1, KRAS G12D, and CypA Deposited 2024-07-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 A1AZV (2R)-2-cyclopentyl-N-[(1M,8S,10R,14S,21M)-22-ethyl-4-hydroxy-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]-2-(N-methylacetamido)acetamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；18-23% PEG3350 + 0.11-0.2M NaCl + 0.10M Bis Tris pH 5.5
|
Resolution 1.42 Å R-free 0.204 |
| 9CT7 Tricomplex of Compound 1, KRAS G12D, and CypA Deposited 2024-07-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 A1AZV (2R)-2-cyclopentyl-N-[(1M,8S,10R,14S,21M)-22-ethyl-4-hydroxy-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]-2-(N-methylacetamido)acetamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；18-23% PEG3350 + 0.11-0.2M NaCl + 0.10M Bis Tris pH 5.5
|
Resolution 1.42 Å R-free 0.204 |
| 9CT8 Tricomplex of Compound 2, KRAS G12D, and CypA Deposited 2024-07-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AZX (2R)-2-amino-N-(2-{[(1R)-1-cyclopentyl-2-{[(1M,8S,10S,14S,21M)-22-ethyl-4-hydroxy-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]amino}-2-oxoethyl](methyl)amino}-2-oxoethyl)-N-methylpropanamide (non-preferred name) × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；22-27% PEG3350 + 0.11-0.20M NaCl + 0.10M MES pH 5.5
|
Resolution 1.28 Å R-free 0.190 |
| 9CT8 Tricomplex of Compound 2, KRAS G12D, and CypA Deposited 2024-07-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AZX (2R)-2-amino-N-(2-{[(1R)-1-cyclopentyl-2-{[(1M,8S,10S,14S,21M)-22-ethyl-4-hydroxy-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]amino}-2-oxoethyl](methyl)amino}-2-oxoethyl)-N-methylpropanamide (non-preferred name) × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；22-27% PEG3350 + 0.11-0.20M NaCl + 0.10M MES pH 5.5
|
Resolution 1.28 Å R-free 0.190 |
| 9CT9 Tricomplex of Compound 3, KRAS G12D, and CypA Deposited 2024-07-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 A1AZY (2R)-2-{(5S)-7-[(2R)-2-aminopropanoyl]-1-oxo-2,7-diazaspiro[4.4]nonan-2-yl}-2-cyclopentyl-N-[(1M,8S,10S,14R,21M)-22-ethyl-4-hydroxy-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]acetamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350 + 0.20M Sodium chloride + 0.10M MES pH 5.5 + 1.25% Glycerol
|
Resolution 1.35 Å R-free 0.185 |
| 9CT9 Tricomplex of Compound 3, KRAS G12D, and CypA Deposited 2024-07-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 A1AZY (2R)-2-{(5S)-7-[(2R)-2-aminopropanoyl]-1-oxo-2,7-diazaspiro[4.4]nonan-2-yl}-2-cyclopentyl-N-[(1M,8S,10S,14R,21M)-22-ethyl-4-hydroxy-21-{2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]acetamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；20% PEG 3350 + 0.20M Sodium chloride + 0.10M MES pH 5.5 + 1.25% Glycerol
|
Resolution 1.35 Å R-free 0.185 |
| 9CTA Tricomplex of RMC-9945, KRAS G12D, and CypA Deposited 2024-07-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AZW (2R)-2-{(5S)-7-[(2R)-3-cyclopropyl-2-(methylamino)propanoyl]-2,7-diazaspiro[4.4]nonan-2-yl}-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1R)-1-methoxyethyl]pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-21-(2,2,2-trifluoroethyl)-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-methylbutanamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；MES 5.5, NaCl, PEG3350
|
Resolution 1.29 Å R-free 0.194 |
| 9CTA Tricomplex of RMC-9945, KRAS G12D, and CypA Deposited 2024-07-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 A1AZW (2R)-2-{(5S)-7-[(2R)-3-cyclopropyl-2-(methylamino)propanoyl]-2,7-diazaspiro[4.4]nonan-2-yl}-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1R)-1-methoxyethyl]pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-21-(2,2,2-trifluoroethyl)-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-methylbutanamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；MES 5.5, NaCl, PEG3350
|
Resolution 1.29 Å R-free 0.194 |
| 9CTB Tri-complex of zoldonrasib (RMC-9805), KRAS G12D, and CypA Deposited 2024-07-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 A1AZZ (2R)-2-cyclopentyl-2-{(5S)-7-[(2R)-3-cyclopropyl-2-(methylamino)propanoyl]-2,7-diazaspiro[4.4]nonan-2-yl}-N-[(2S,6R,8S,10R,14S,21M)-21-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-22-(2,2,2-trifluoroethyl)-5,16-dioxa-2,10,22,28-tetraazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),20,23,26-tetraen-8-yl]acetamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M MES 5.5, 20% PEG3350, 0.1 M NaCl
|
Resolution 1.29 Å R-free 0.194 |
| 9CTB Tri-complex of zoldonrasib (RMC-9805), KRAS G12D, and CypA Deposited 2024-07-24 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 A1AZZ (2R)-2-cyclopentyl-2-{(5S)-7-[(2R)-3-cyclopropyl-2-(methylamino)propanoyl]-2,7-diazaspiro[4.4]nonan-2-yl}-N-[(2S,6R,8S,10R,14S,21M)-21-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1R)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-22-(2,2,2-trifluoroethyl)-5,16-dioxa-2,10,22,28-tetraazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),20,23,26-tetraen-8-yl]acetamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M MES 5.5, 20% PEG3350, 0.1 M NaCl
|
Resolution 1.29 Å R-free 0.194 |
| 9E3S Tricomplex of RMC-9945, KRAS G12N, and CypA Deposited 2024-10-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 A1BEA (2R)-2-{(5S)-7-[(2R,3R)-3-cyclopropyl-1-methylaziridine-2-carbonyl]-2,7-diazaspiro[4.4]nonan-2-yl}-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1R)-1-methoxyethyl]pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-21-(2,2,2-trifluoroethyl)-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-methylbutanamide (non-preferred name) × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M MES 6 pH,
0.1-0.2 M NaCl,
21-26 %w/v PEG 3350
|
Resolution 1.08 Å R-free 0.178 |
| 9E3S Tricomplex of RMC-9945, KRAS G12N, and CypA Deposited 2024-10-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–165（165 aa）
|
Not recorded | GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 MG MAGNESIUM ION × 1 CL CHLORIDE ION × 1 A1BEA (2R)-2-{(5S)-7-[(2R,3R)-3-cyclopropyl-1-methylaziridine-2-carbonyl]-2,7-diazaspiro[4.4]nonan-2-yl}-N-[(1P,7S,9S,13S,20M)-20-{5-(4-cyclopropylpiperazin-1-yl)-2-[(1R)-1-methoxyethyl]pyridin-3-yl}-17,17-dimethyl-8,14-dioxo-21-(2,2,2-trifluoroethyl)-15-oxa-4-thia-9,21,27,28-tetraazapentacyclo[17.5.2.1~2,5~.1~9,13~.0~22,26~]octacosa-1(24),2,5(28),19,22,25-hexaen-7-yl]-3-methylbutanamide (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；0.1 M MES 6 pH,
0.1-0.2 M NaCl,
21-26 %w/v PEG 3350
|
Resolution 1.08 Å R-free 0.178 |
| 9GHY Cyclophilin A in complex with Sanglifehrin A analogue (2R,3S,7S,10S,E)-10-(3-aminopropyl)-2,7-dimethylspiro[3,8,11-triaza-1(2,7)-quinolina-5(3,1)-pyridazinacyclopentadecaphanene-13,5'-[1,3]dioxan]-14-ene-4,6,9,12-tetraone Deposited 2024-08-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–165（165 aa）
|
Not recorded | A1ILH (2R,3S,7S,10S,E)-10-(3-aminopropyl)-2,7-dimethylspiro[3,8,11-triaza-1(2,7)-quinolina-5(3,1)-pyridazinacyclopentadecaphanene-13,5'-[1,3]dioxan]-14-ene-4,6,9,12-tetraone × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；28% PEG-3350, 0.1 M Tris-HCl pH 8.8
|
Resolution 1.15 Å R-free 0.149 |
| 9YOW Crystal structure of GMPPNP bound KRAS G12C in complex with CYPA and RMC-4791 Deposited 2025-10-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–165（165 aa）
|
Not recorded | MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 A1CYT 1-cyano-N-[(2S)-1-{[(1M,8S,10S,14S,21M)-22-ethyl-4-hydroxy-21-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-N-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；0.1 M Tris pH 8.0, 0.2 M NaCl, 20% PEG 6000
|
Resolution 1.57 Å R-free 0.245 |
| 9YOW Crystal structure of GMPPNP bound KRAS G12C in complex with CYPA and RMC-4791 Deposited 2025-10-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–165（165 aa）
|
Not recorded | MG MAGNESIUM ION × 1 GNP PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER × 1 A1CYT 1-cyano-N-[(2S)-1-{[(1M,8S,10S,14S,21M)-22-ethyl-4-hydroxy-21-{2-[(1S)-1-methoxyethyl]pyridin-3-yl}-18,18-dimethyl-9,15-dioxo-16-oxa-10,22,28-triazapentacyclo[18.5.2.1~2,6~.1~10,14~.0~23,27~]nonacosa-1(25),2(29),3,5,20,23,26-heptaen-8-yl]amino}-3-methyl-1-oxobutan-2-yl]-N-methylcyclopropane-1-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；298.15 K；0.1 M Tris pH 8.0, 0.2 M NaCl, 20% PEG 6000
|
Resolution 1.57 Å R-free 0.245 |
183 other PDB entries and 255 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | PPIA_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–165； UniProt 1–164 Author chain B； PDBConstruct 1–165； UniProt 1–164 Author chain E； PDBConstruct 1–165； UniProt 1–164 Author chain F； PDBConstruct 1–165； UniProt 1–164 |
