Growth factor receptor-bound protein 2
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 × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain A； UniProt 54–153 Chain E； UniProt 54–153 | Mutation：W121G | SER-PTR-VAL-ASN-VAL-GLN × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000 | Resolution 2.60 Å R-free 0.294 |
| 2 | Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain B； UniProt 54–153 Chain C； UniProt 54–153 | Mutation：W121G | SER-PTR-VAL-ASN-VAL-GLN × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000 | Resolution 2.60 Å R-free 0.294 |
| 3 | Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain G； UniProt 54–153 Chain H； UniProt 54–153 | Mutation：W121G | SER-PTR-VAL-ASN-VAL-GLN × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000 | Resolution 2.60 Å R-free 0.294 |
| 4 | Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain K； UniProt 54–153 Chain L； UniProt 54–153 | Mutation：W121G | SER-PTR-VAL-ASN-VAL-GLN × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000 | Resolution 2.60 Å R-free 0.294 |
| 5 | Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain O； UniProt 54–153 Chain P； UniProt 54–153 | Mutation：W121G | SER-PTR-VAL-ASN-VAL-GLN × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000 | Resolution 2.60 Å R-free 0.294 |
| 6 | Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain U； UniProt 54–153 Chain V； UniProt 54–153 | Mutation：W121G | SER-PTR-VAL-ASN-VAL-GLN × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000 | Resolution 2.60 Å R-free 0.294 |
| 7 | Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain Y； UniProt 54–153 Chain Z； UniProt 54–153 | Mutation：W121G | SER-PTR-VAL-ASN-VAL-GLN × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000 | Resolution 2.60 Å R-free 0.294 |
| 8 | Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count | Chain c； UniProt 54–153 Chain d； UniProt 54–153 | Mutation：W121G | SER-PTR-VAL-ASN-VAL-GLN × 2 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.335M Potassium thiocyanate, 31% (w/v) PEG 8000 | Resolution 2.60 Å R-free 0.294 |
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 5CDW | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 1AZE NMR STRUCTURE OF THE COMPLEX BETWEEN THE C32S-Y7V MUTANT OF THE NSH3 DOMAIN OF GRB2 WITH A PEPTIDE FROM SOS, 10 STRUCTURES Deposited 1997-11-17 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–56（56 aa）
Fragment：N-TERMINAL SH3 DOMAIN, RESIDUES 1 - 55
|
Mutation：Y7V, C32S | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6；293 K；Ionic strength (raw mmCIF value) NACL 100mM；Pressure 1
NMR sample composition
H2O, PHOSPHATE BUFFER 20MM, NACL 100MM
|
Resolution not provided |
| 1BMB GRB2-SH2 DOMAIN IN COMPLEX WITH KPFY*VNVEF (PKF270-974) Deposited 1998-07-23 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
46–168（123 aa）
Fragment：SH2 DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PROTEIN (15MG/ML IN 100MM SODIUM CHLORIDE, 0.02% SODIUM AZIDE) WAS CRYSTALLIZED FROM 46% SATURATED AMMONIUM SULFATE, 100MM SODIUM MES PH 6.5, IN PRESENCE OF A 2-FOLD EXCESS OF LIGAND
|
Resolution 1.80 Å R-free 0.218 |
| 1BMB GRB2-SH2 DOMAIN IN COMPLEX WITH KPFY*VNVEF (PKF270-974) Deposited 1998-07-23 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
46–168（123 aa）
Fragment：SH2 DOMAIN
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PROTEIN (15MG/ML IN 100MM SODIUM CHLORIDE, 0.02% SODIUM AZIDE) WAS CRYSTALLIZED FROM 46% SATURATED AMMONIUM SULFATE, 100MM SODIUM MES PH 6.5, IN PRESENCE OF A 2-FOLD EXCESS OF LIGAND
|
Resolution 1.80 Å R-free 0.218 |
| 1CJ1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE Deposited 1999-04-21 | 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
57–152（96 aa）
Fragment：SH2 DOMAIN
Chain B
57–152（96 aa）
Fragment：SH2 DOMAIN
|
Not recorded | C78 [1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；0.1 M HEPES.NA PH 7.5 1.4 M NA- ACETATE, VAPOR DIFFUSION
|
Resolution 3.00 Å R-free 0.317 |
| 1CJ1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE Deposited 1999-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
57–152（96 aa）
Fragment：SH2 DOMAIN
Chain D
57–152（96 aa）
Fragment：SH2 DOMAIN
|
Not recorded | C78 [1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；0.1 M HEPES.NA PH 7.5 1.4 M NA- ACETATE, VAPOR DIFFUSION
|
Resolution 3.00 Å R-free 0.317 |
| 1CJ1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE Deposited 1999-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain E
57–152（96 aa）
Fragment：SH2 DOMAIN
Chain F
57–152（96 aa）
Fragment：SH2 DOMAIN
|
Not recorded | C78 [1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；0.1 M HEPES.NA PH 7.5 1.4 M NA- ACETATE, VAPOR DIFFUSION
|
Resolution 3.00 Å R-free 0.317 |
| 1CJ1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE Deposited 1999-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain G
57–152（96 aa）
Fragment：SH2 DOMAIN
Chain H
57–152（96 aa）
Fragment：SH2 DOMAIN
|
Not recorded | C78 [1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；0.1 M HEPES.NA PH 7.5 1.4 M NA- ACETATE, VAPOR DIFFUSION
|
Resolution 3.00 Å R-free 0.317 |
| 1CJ1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE Deposited 1999-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain I
57–152（96 aa）
Fragment：SH2 DOMAIN
Chain J
57–152（96 aa）
Fragment：SH2 DOMAIN
|
Not recorded | C78 [1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；0.1 M HEPES.NA PH 7.5 1.4 M NA- ACETATE, VAPOR DIFFUSION
|
Resolution 3.00 Å R-free 0.317 |
| 1CJ1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN (HUMAN) COMPLEXED WITH A PHOSPHOTYROSYL DERIVATIVE Deposited 1999-04-21 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain K
57–152（96 aa）
Fragment：SH2 DOMAIN
Chain L
57–152（96 aa）
Fragment：SH2 DOMAIN
|
Not recorded | C78 [1-[1-(6-CARBAMOYL-CYCLOHEX-2-ENYLCARBAMOYL)-CYCLOHEXYLCARBAMOYL]-2-(4-PHOSPHONOOXY-PHENYL)- ETHYL]-CARBAMIC ACID 3-AMINOBENZYLESTER × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；0.1 M HEPES.NA PH 7.5 1.4 M NA- ACETATE, VAPOR DIFFUSION
|
Resolution 3.00 Å R-free 0.317 |
| 1FHS THE THREE-DIMENSIONAL SOLUTION STRUCTURE OF THE SRC HOMOLOGY DOMAIN-2 OF THE GROWTH FACTOR RECEPTOR BOUND PROTEIN-2, NMR, 18 STRUCTURES Deposited 1997-06-12 | Different construct Different mutation/modification 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
53–163（111 aa）
Fragment：SH2 DOMAIN
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 5.3；298 K
|
Resolution not provided |
| 1GCQ CRYSTAL STRUCTURE OF VAV AND GRB2 SH3 DOMAINS Deposited 2000-08-08 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
159–217（59 aa）
Fragment：C-TERMINAL SH3 DOMAIN
Chain B
159–217（59 aa）
Fragment：C-TERMINAL SH3 DOMAIN
|
Not recorded | MRD (4R)-2-METHYLPENTANE-2,4-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293.2 K；2-methyl-2,4-pentanediol, imidazole, magnesium chloride, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.2K
|
Resolution 1.68 Å R-free 0.235 |
| 1GFC SOLUTION STRUCTURE AND LIGAND-BINDING SITE OF THE C-TERMINAL SH3 DOMAIN OF GRB2 Deposited 1994-06-13 | Different construct Different mutation/modification 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
159–215（57 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1GFD SOLUTION STRUCTURE AND LIGAND-BINDING SITE OF THE C-TERMINAL SH3 DOMAIN OF GRB2 Deposited 1994-06-13 | Different construct Different mutation/modification 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
159–215（57 aa）
|
Not recorded | No recorded non-water small molecule | SOLUTION NMR mmCIF provides none of the parsed conditions | Resolution not provided |
| 1GHU NMR solution structure of growth factor receptor-bound protein 2 (GRB2) SH2 domain, 24 structures Deposited 1996-08-05 | Different construct Different mutation/modification 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
60–158（99 aa）
Fragment：SH2 DOMAIN
|
Mutation：RESIDUES 58-59, 159-164 ARE CLONING ARTIFACTS | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.2；298 K
|
Resolution not provided |
| 1GRI GRB2 Deposited 1995-02-28 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
1–217（217 aa）
Chain B
1–217（217 aa）
|
Not recorded | No recorded non-water small molecule | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.10 Å |
| 1IO6 GROWTH FACTOR RECEPTOR-BOUND PROTEIN 2 (GRB2) C-TERMINAL SH3 DOMAIN COMPLEXED WITH A LIGAND PEPTIDE (NMR, MINIMIZED MEAN STRUCTURE) Deposited 2001-01-25 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
159–215（57 aa）
Fragment：C-TERMINAL SH3(RESIDUE 159-215)
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7.2；298 K
|
Resolution not provided |
| 1JYR Xray Structure of Grb2 SH2 Domain Complexed with a Phosphorylated Peptide Deposited 2001-09-13 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
60–151（92 aa）
Fragment：SH2 Domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；ammonium phosphate, PEG400, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.55 Å R-free 0.228 |
| 1JYR Xray Structure of Grb2 SH2 Domain Complexed with a Phosphorylated Peptide Deposited 2001-09-13 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
60–151（92 aa）
Fragment：SH2 Domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；ammonium phosphate, PEG400, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 1.55 Å R-free 0.228 |
| 1JYU Xray Structure of Grb2 SH2 Domain Deposited 2001-09-13 | 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
60–151（92 aa）
Fragment：SH2 Domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG4000, glycerol, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.75 Å R-free 0.287 |
| 1JYU Xray Structure of Grb2 SH2 Domain Deposited 2001-09-13 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 8 PDB declaration: octameric |
Chain A
60–151（92 aa）
Fragment：SH2 Domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；291 K；PEG4000, glycerol, pH 6, VAPOR DIFFUSION, HANGING DROP, temperature 291K
|
Resolution 2.75 Å R-free 0.287 |
| 1QG1 GROWTH FACTOR RECEPTOR BINDING PROTEIN SH2 DOMAIN COMPLEXED WITH AN SHC-DERIVED PEPTIDE Deposited 1999-04-19 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
58–159（102 aa）
Fragment：SH2
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.3；301 K
|
Resolution not provided |
| 1X0N NMR structure of growth factor receptor binding protein SH2 domain complexed with the inhibitor Deposited 2005-03-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
58–159（102 aa）
Fragment：SH2 DOMAIN
|
Not recorded | DTF 4-[(10S,14S,18S)-18-(2-AMINO-2-OXOETHYL)-14-(1-NAPHTHYLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL]BENZYLPHOSPHONIC ACID × 1 |
SOLUTION NMR
NMR measurement conditions
pH 6.3；298 K；Pressure 1
NMR sample composition
1mM SH2 U-13C, 15N; 20mM sodium phosphate; 150mM NaCl | 90% H2O/10% D2O
|
Resolution not provided |
| 2AOA Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | 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
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG3350, sodium chloride, sodium acetate, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.99 Å R-free 0.307 |
| 2AOA Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different mutation/modification 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
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 1 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG3350, sodium chloride, sodium acetate, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.99 Å R-free 0.307 |
| 2AOA Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
Chain B
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 3 P33 3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG3350, sodium chloride, sodium acetate, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.99 Å R-free 0.307 |
| 2AOB Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | 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
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG 3350, sodium acetate, sodium chloride, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.80 Å R-free 0.293 |
| 2AOB Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different mutation/modification 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
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG 3350, sodium acetate, sodium chloride, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.80 Å R-free 0.293 |
| 2AOB Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different mutation/modification 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
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG 3350, sodium acetate, sodium chloride, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.80 Å R-free 0.293 |
| 2AOB Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different mutation/modification 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
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG 3350, sodium acetate, sodium chloride, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.80 Å R-free 0.293 |
| 2AOB Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain C
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
Chain D
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG 3350, sodium acetate, sodium chloride, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.80 Å R-free 0.293 |
| 2AOB Crystal structures of a high-affinity macrocyclic peptide mimetic in complex with the Grb2 SH2 domain Deposited 2005-08-12 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
Chain B
55–153（99 aa）
Fragment：SH2 (residues 55 - 153)
|
Not recorded | S1S 2-(4-((9S,10S,14S,Z)-18-(2-AMINO-2-OXOETHYL)-9-(CARBOXYMETHYL)-14-(NAPHTHALEN-1-YLMETHYL)-8,17,20-TRIOXO-7,16,19-TRIAZASPIRO[5.14]ICOS-11-EN-10-YL)PHENYL)MALONIC ACID × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.7；298 K；PEG 3350, sodium acetate, sodium chloride, pH 5.7, VAPOR DIFFUSION, temperature 298K
|
Resolution 1.80 Å R-free 0.293 |
| 2H5K Crystal Structure of Complex Between the Domain-Swapped Dimeric Grb2 SH2 Domain and Shc-Derived Ligand, Ac-NH-pTyr-Val-Asn-NH2 Deposited 2006-05-26 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
53–162（110 aa）
Fragment：SH2 Domain
Chain B
53–162（110 aa）
Fragment：SH2 Domain
|
Not recorded | CAC CACODYLATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；Protein-ligand solution in 25 mM sodium cacodylate, pH 6.0 mixed with equal volume of 0.1 M sodium cacodylate, 0.1 M calcium acetate, 18% PEG 8000, pH 6.0., VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 3.25 Å R-free 0.300 |
| 2HUW X-ray crystal structure of the Grb2 SH2 domain complexed to a constrained and cyclopropane-derived ligand Deposited 2006-07-27 | 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
53–162（110 aa）
Fragment：SH2 domain
|
Not recorded | YVN N-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-L-valyl-L-aspartamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Ligand (cpYVN) was added to a 1.5 molar excess to a solution of 50 mg/ml Grb2-SH2 in 50 mM sodium cacodylate at PH 6.0. This solution was mixed with an equal volume of 4% (v/v) PEG 400, 2.0 M (NH4)2PO4., VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.227 |
| 2HUW X-ray crystal structure of the Grb2 SH2 domain complexed to a constrained and cyclopropane-derived ligand Deposited 2006-07-27 | Different construct Different mutation/modification 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
53–162（110 aa）
Fragment：SH2 domain
|
Not recorded | YVN N-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-L-valyl-L-aspartamide × 1 PO4 PHOSPHATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；Ligand (cpYVN) was added to a 1.5 molar excess to a solution of 50 mg/ml Grb2-SH2 in 50 mM sodium cacodylate at PH 6.0. This solution was mixed with an equal volume of 4% (v/v) PEG 400, 2.0 M (NH4)2PO4., VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.90 Å R-free 0.227 |
| 2VVK Grb2 SH3C (1) Deposited 2008-06-09 | 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
161–214（54 aa）
Fragment：SH3 DOMAIN, RESIDUES 161-214
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 4.6；8% PEG 4K, 0.1M NAACETATE PH 4.6
|
Resolution 1.60 Å R-free 0.178 |
| 2VWF Grb2 SH3C (2) Deposited 2008-06-24 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
159–214（56 aa）
Fragment：SH3 DOMAIN, RESIDUES 159-214
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7；2M TRI-AMMONIUM CITRATE, 0.1M BIS-TRIS PROPANE PH7, pH 7.0
|
Resolution 1.58 Å R-free 0.219 |
| 2W0Z Grb2 SH3C (3) Deposited 2008-10-13 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
159–214（56 aa）
Fragment：SH3 DOMAIN, RESIDUES 159-214
|
Mutation：YES | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；0.7 M TRISODIUM CITRATE, 0.1 M TRIS PH 8.5
|
Resolution 1.70 Å R-free 0.206 |
| 3C7I X-RAY crystal structure of the complex between the grb2-sh2 domain and a flexible ligand, FPTVN. Deposited 2008-02-07 | 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
53–162（110 aa）
|
Not recorded | TVN N-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-valyl-L-aspartamide × 2 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5；293 K；LIGAND (FPTVN) was added in a 1.5 molar excess to 15 MG/ML GRB2-SH2 in pure water.
This solution was mixed with an equal volume of 4.0 m sodium formate., pH 5.00, VAPOR DIFFUSION, HANGING DROP, temperature 293KK
|
Resolution 1.70 Å R-free 0.234 |
| 3IMD Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-Q-N-NH2 Tripeptide Mimic Deposited 2009-08-10 | 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
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | FYQ N~2~-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-glutaminyl-L-aspartamide × 1 CL CHLORIDE ION × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyphilized powder form was dissolved in a 9.1 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 3 uL of this solution was mixed with 4 uL of 0.2 M MgCl2 x 6H2O, 30% w/v PEG MW4000, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.237 |
| 3IMD Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-Q-N-NH2 Tripeptide Mimic Deposited 2009-08-10 | Different construct Different mutation/modification 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
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | FYQ N~2~-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-glutaminyl-L-aspartamide × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyphilized powder form was dissolved in a 9.1 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 3 uL of this solution was mixed with 4 uL of 0.2 M MgCl2 x 6H2O, 30% w/v PEG MW4000, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.237 |
| 3IMD Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-Q-N-NH2 Tripeptide Mimic Deposited 2009-08-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：SH2 domain
Chain B
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | FYQ N~2~-{(2R)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-glutaminyl-L-aspartamide × 2 CL CHLORIDE ION × 4 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyphilized powder form was dissolved in a 9.1 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 3 uL of this solution was mixed with 4 uL of 0.2 M MgCl2 x 6H2O, 30% w/v PEG MW4000, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.237 |
| 3IMJ Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pTyr-Ile-Asn-NH2 Tripeptide Mimic Deposited 2009-08-10 | 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
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | AYI (1R,2S,3R,1S',1S")Phosphoric acid mono(4-{2-[1-(1,2-dicarbamoylethylcarbamoyl)-3-carbamoylpropylcarbamoyl]-3-methylcarbamoylcyclopropyl}phenyl) ester × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；Ligand in lyophilized powder form was dissolved in a 11.2 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 4 uL of this solution was mixed with 3 uL of 0.2 M ammonium acetate, 0.1 M sodium acetate, 30% v/v PEG MW4000, pH 4.6 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.02 Å R-free 0.229 |
| 3IMJ Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pTyr-Ile-Asn-NH2 Tripeptide Mimic Deposited 2009-08-10 | Different construct Different mutation/modification 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
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | AYI (1R,2S,3R,1S',1S")Phosphoric acid mono(4-{2-[1-(1,2-dicarbamoylethylcarbamoyl)-3-carbamoylpropylcarbamoyl]-3-methylcarbamoylcyclopropyl}phenyl) ester × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；Ligand in lyophilized powder form was dissolved in a 11.2 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 4 uL of this solution was mixed with 3 uL of 0.2 M ammonium acetate, 0.1 M sodium acetate, 30% v/v PEG MW4000, pH 4.6 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.02 Å R-free 0.229 |
| 3IMJ Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pTyr-Ile-Asn-NH2 Tripeptide Mimic Deposited 2009-08-10 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：SH2 domain
Chain B
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | AYI (1R,2S,3R,1S',1S")Phosphoric acid mono(4-{2-[1-(1,2-dicarbamoylethylcarbamoyl)-3-carbamoylpropylcarbamoyl]-3-methylcarbamoylcyclopropyl}phenyl) ester × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 4.6；298 K；Ligand in lyophilized powder form was dissolved in a 11.2 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 4 uL of this solution was mixed with 3 uL of 0.2 M ammonium acetate, 0.1 M sodium acetate, 30% v/v PEG MW4000, pH 4.6 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.02 Å R-free 0.229 |
| 3IN7 Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pY-Q-N-NH2 Tripeptide Mimic Deposited 2009-08-11 | 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
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | AYQ N~2~-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-D-glutaminyl-D-aspartamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Ligand in lyophilized powder form was dissolved in a 7.6 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1.7:1. 3.5 uL of this solution was mixed with 3.5 uL of 0.1 M HEPES, 20% w/v PEG MW10,000, pH 7.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after two weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.250 |
| 3IN7 Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pY-Q-N-NH2 Tripeptide Mimic Deposited 2009-08-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | AYQ N~2~-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-D-glutaminyl-D-aspartamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Ligand in lyophilized powder form was dissolved in a 7.6 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1.7:1. 3.5 uL of this solution was mixed with 3.5 uL of 0.1 M HEPES, 20% w/v PEG MW10,000, pH 7.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after two weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.250 |
| 3IN7 Crystal Structure of the Grb2 SH2 Domain in Complex with a Cyclopropyl-constrained Ac-pY-Q-N-NH2 Tripeptide Mimic Deposited 2009-08-11 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：SH2 domain
Chain C
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | AYQ N~2~-({(1R,2R,3S)-2-(methylcarbamoyl)-3-[4-(phosphonooxy)phenyl]cyclopropyl}carbonyl)-D-glutaminyl-D-aspartamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Ligand in lyophilized powder form was dissolved in a 7.6 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1.7:1. 3.5 uL of this solution was mixed with 3.5 uL of 0.1 M HEPES, 20% w/v PEG MW10,000, pH 7.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after two weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.250 |
| 3IN8 Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pTyr-Ile-Asn-NH2 Tripeptide Mimic Deposited 2009-08-11 | 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
53–163（111 aa）
Fragment：SH2 domain
|
Not recorded | FYI N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-isoleucyl-L-aspartamide × 2 FMT FORMIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；Ligand in lyophilized powder form was dissolved in a 15.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1. 3.5 uL of this solution was mixed with 3.5 uL of 5.0 M sodium formate, pH 7.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after six weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.70 Å R-free 0.211 |
| 3KFJ Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-E-N-NH2 Tripeptide Mimic Deposited 2009-10-27 | 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
53–163（111 aa）
Fragment：SH2 domain, residues 53-163
|
Not recorded | YEN N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-alpha-glutamyl-L-aspartamide × 1 CL CHLORIDE ION × 2 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyophilized powder form was dissolved in a 9.5 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 4uL of this solution was mixed with 3uL of 0.1 M MgCl2 x 6H2O, 30% w/v PEG MW4000, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.02 Å R-free 0.230 |
| 3KFJ Crystal Structure of the Grb2 SH2 Domain in Complex with a Flexible Ac-pY-E-N-NH2 Tripeptide Mimic Deposited 2009-10-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：SH2 domain, residues 53-163
|
Not recorded | YEN N-{(2S)-4-(methylamino)-4-oxo-2-[4-(phosphonooxy)benzyl]butanoyl}-L-alpha-glutamyl-L-aspartamide × 2 CL CHLORIDE ION × 4 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyophilized powder form was dissolved in a 9.5 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 2:1. 4uL of this solution was mixed with 3uL of 0.1 M MgCl2 x 6H2O, 30% w/v PEG MW4000, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex in the presence of the above-mentioned solution after four weeks at room temperature., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.02 Å R-free 0.230 |
| 3MXC Structures of Grb2-SH2 Domain and AICD peptide Complexes Reveal a Conformational Switch and Their Functional Implications. Deposited 2010-05-07 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
55–152（98 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
293 K；0.1 M Tris ,0.1M Bicine, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.00 Å R-free 0.244 |
| 3MXY Structures of Grb2-SH2 Domain and AICD peptide Complexes Reveal a Conformational Switch and Their Functional Implications. Deposited 2010-05-08 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
55–152（98 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M Tris ,0.1M Bicine, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 2.30 Å R-free 0.252 |
| 3N7Y Crystal Structure of the Grb2 SH2 Domain in Complex with a 20-Membered Macrocyclic Ligand Having the Sequence pYVNV Deposited 2010-05-27 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
55–152（98 aa）
Fragment：SH2 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ligand in lyohpilized power form was dissolved in a 10.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:2. 3.5 uL of this solution was mixed with 3.5 uL of 20% v/v isopropanol, 20% w/v polyethylene glycol MW 4,000, 0.1 M sodium citrate dihydrate, pH 5.6 to create the hanging drop, which yielded crystals of the protein-ligand complex after two weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298KK
|
Resolution 2.02 Å R-free 0.222 |
| 3N7Y Crystal Structure of the Grb2 SH2 Domain in Complex with a 20-Membered Macrocyclic Ligand Having the Sequence pYVNV Deposited 2010-05-27 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
55–152（98 aa）
Fragment：SH2 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ligand in lyohpilized power form was dissolved in a 10.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:2. 3.5 uL of this solution was mixed with 3.5 uL of 20% v/v isopropanol, 20% w/v polyethylene glycol MW 4,000, 0.1 M sodium citrate dihydrate, pH 5.6 to create the hanging drop, which yielded crystals of the protein-ligand complex after two weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298KK
|
Resolution 2.02 Å R-free 0.222 |
| 3N7Y Crystal Structure of the Grb2 SH2 Domain in Complex with a 20-Membered Macrocyclic Ligand Having the Sequence pYVNV Deposited 2010-05-27 | Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
55–152（98 aa）
Fragment：SH2 domain
Chain C
55–152（98 aa）
Fragment：SH2 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ligand in lyohpilized power form was dissolved in a 10.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:2. 3.5 uL of this solution was mixed with 3.5 uL of 20% v/v isopropanol, 20% w/v polyethylene glycol MW 4,000, 0.1 M sodium citrate dihydrate, pH 5.6 to create the hanging drop, which yielded crystals of the protein-ligand complex after two weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298KK
|
Resolution 2.02 Å R-free 0.222 |
| 3N7Y Crystal Structure of the Grb2 SH2 Domain in Complex with a 20-Membered Macrocyclic Ligand Having the Sequence pYVNV Deposited 2010-05-27 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
55–152（98 aa）
Fragment：SH2 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ligand in lyohpilized power form was dissolved in a 10.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:2. 3.5 uL of this solution was mixed with 3.5 uL of 20% v/v isopropanol, 20% w/v polyethylene glycol MW 4,000, 0.1 M sodium citrate dihydrate, pH 5.6 to create the hanging drop, which yielded crystals of the protein-ligand complex after two weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298KK
|
Resolution 2.02 Å R-free 0.222 |
| 3N7Y Crystal Structure of the Grb2 SH2 Domain in Complex with a 20-Membered Macrocyclic Ligand Having the Sequence pYVNV Deposited 2010-05-27 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
55–152（98 aa）
Fragment：SH2 domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Ligand in lyohpilized power form was dissolved in a 10.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:2. 3.5 uL of this solution was mixed with 3.5 uL of 20% v/v isopropanol, 20% w/v polyethylene glycol MW 4,000, 0.1 M sodium citrate dihydrate, pH 5.6 to create the hanging drop, which yielded crystals of the protein-ligand complex after two weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298KK
|
Resolution 2.02 Å R-free 0.222 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
52–162（111 aa）
Fragment：SH2 domain
Chain E
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | CL CHLORIDE ION × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain B
52–162（111 aa）
Fragment：SH2 domain
Chain D
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain C
52–162（111 aa）
Fragment：SH2 domain
Chain F
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | GOL GLYCEROL × 3 MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | MG MAGNESIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain E
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N84 Crystal Structure of the Grb2 SH2 Domain in Complex with a 23-Membered Macrocyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 9 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain F
52–162（111 aa）
Fragment：SH2 domain
|
Not recorded | GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyoophilized powder form was dissolved in a 8.0 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 30% w/v polyethylene glycol MW 4000, 0.2 M magnesium chloride hexahydrate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded usable crystals after 8 weeks., VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.223 |
| 3N8M Crystal Structure of the Grb2 SH2 Domain in Complex with An Acyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-28 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：Grb2 SH2 domain, residues 55-153
|
Not recorded | GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyophilized powder form was dissolved in a 7.2 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 12% v/v glycerol, 1.5 M ammonium sulfate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex after 8 weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.224 |
| 3N8M Crystal Structure of the Grb2 SH2 Domain in Complex with An Acyclic Ligand Having the Sequence pYVNVP Deposited 2010-05-28 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
53–163（111 aa）
Fragment：Grb2 SH2 domain, residues 55-153
|
Not recorded | GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；Ligand in lyophilized powder form was dissolved in a 7.2 mg/mL solution of Grb2 SH2 in water such to give a protein/ligand molar ratio of 1:1.7. 4 uL of this solution was mixed with 3 uL of 12% v/v glycerol, 1.5 M ammonium sulfate, 0.1 M TRIS, pH 8.5 to create the hanging drop, which yielded crystals of the protein-ligand complex after 8 weeks, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.00 Å R-free 0.224 |
| 3OV1 Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2010-09-15 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | GOL GLYCEROL × 2 FMT FORMIC ACID × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES, 20% w/v Polyethylene Glycol 10,000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.60 Å R-free 0.214 |
| 3OV1 Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2010-09-15 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | GOL GLYCEROL × 4 FMT FORMIC ACID × 2 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES, 20% w/v Polyethylene Glycol 10,000, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.60 Å R-free 0.214 |
| 3OVE Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2010-09-16 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.2 M magnesium chloride hexahydrate, 0.1 M TRIS,30% w/v polyethylene glycol 4,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.82 Å R-free 0.260 |
| 3OVE Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2010-09-16 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；298 K；0.2 M magnesium chloride hexahydrate, 0.1 M TRIS,30% w/v polyethylene glycol 4,000, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.82 Å R-free 0.260 |
| 3S8L Protein-Ligand Interactions: Thermodynamic Effects Associated with Increasing Hydrophobic Surface Area Deposited 2011-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | CL CHLORIDE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES, 3.5 M sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.71 Å R-free 0.256 |
| 3S8N Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2011-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | GOL GLYCEROL × 3 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES, 4.3 M sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.71 Å R-free 0.244 |
| 3S8N Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2011-05-29 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | GOL GLYCEROL × 6 CL CHLORIDE ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES, 4.3 M sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.71 Å R-free 0.244 |
| 3S8O Crystal Structure of the Grb2 SH2 Domain in Complex with a pYXN-Derived Tripeptide Deposited 2011-05-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：unp residues 53-163
|
Not recorded | NA SODIUM ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；0.1 M HEPES, 5.0 M sodium chloride, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 1.85 Å R-free 0.201 |
| 3WA4 Grb2 SH2 domain/CD28-derived peptide complex Deposited 2013-04-23 | 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
60–152（93 aa）
Fragment：SH2 domain, UNP resideus 57-152
|
Not recorded | CD CADMIUM ION × 1 ACY ACETIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES, 1.25M sodium acetate, 0.1M cadmium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.35 Å R-free 0.209 |
| 3WA4 Grb2 SH2 domain/CD28-derived peptide complex Deposited 2013-04-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
60–152（93 aa）
Fragment：SH2 domain, UNP resideus 57-152
|
Not recorded | CD CADMIUM ION × 1 ACY ACETIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1M HEPES, 1.25M sodium acetate, 0.1M cadmium sulfate, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.35 Å R-free 0.209 |
| 4P9V Grb2 SH2 complexed with a pTyr-Ac6cN-Asn tripeptide Deposited 2014-04-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：UNP residues 53-163
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；0.2 M magnesium chloride hexahydrate, 0.1 M TRIS hydrochloride, 30% w/v polyethylene glycol 4000
|
Resolution 1.64 Å R-free 0.257 |
| 4P9Z Grb2 SH2 complexed with a pTyr-Ac6c-Asn tripeptide Deposited 2014-04-06 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
|
Not recorded | GOL GLYCEROL × 1 ACT ACETATE ION × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；0.2 M sodium acetate trihydrate, 0.1 M TRIS hydrochloride, 30% w/v polyethylene glycol 4000
|
Resolution 1.80 Å R-free 0.239 |
| 4P9Z Grb2 SH2 complexed with a pTyr-Ac6c-Asn tripeptide Deposited 2014-04-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric |
Chain A
53–163（111 aa）
|
Not recorded | GOL GLYCEROL × 2 ACT ACETATE ION × 4 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；0.2 M sodium acetate trihydrate, 0.1 M TRIS hydrochloride, 30% w/v polyethylene glycol 4000
|
Resolution 1.80 Å R-free 0.239 |
| 6ICG Grb2 SH2 domain in phosphopeptide free form Deposited 2018-09-06 | 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
60–152（93 aa）
|
Not recorded | SO4 SULFATE ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Sodium chloride, 0.1 M HEPES (pH 7.5), 1.6 M Ammonium sulfate
|
Resolution 1.15 Å R-free 0.169 |
| 6ICG Grb2 SH2 domain in phosphopeptide free form Deposited 2018-09-06 | Different construct Different mutation/modification 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
60–152（93 aa）
|
Not recorded | SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；0.1 M Sodium chloride, 0.1 M HEPES (pH 7.5), 1.6 M Ammonium sulfate
|
Resolution 1.15 Å R-free 0.169 |
| 6ICH Grb2 SH2 domain in domain swapped dimer form Deposited 2018-09-06 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
60–152（93 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1 M MES monohydrate (pH 6.5), 12% PEG 20,000
|
Resolution 2.00 Å R-free 0.242 |
| 6SDF N-terminal SH3 domain of Grb2 protein Deposited 2019-07-26 | 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
2–59（58 aa）
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 5 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M Hepes, 55% (v/v) MPD
|
Resolution 2.50 Å R-free 0.210 |
| 6SDF N-terminal SH3 domain of Grb2 protein Deposited 2019-07-26 | Different construct Different mutation/modification 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
2–59（58 aa）
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1 M Hepes, 55% (v/v) MPD
|
Resolution 2.50 Å R-free 0.210 |
| 6VK2 NMR solution structure of Grb2-SH2 domain at pH 7 Deposited 2020-01-18 | Different construct Different mutation/modification 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
55–150（96 aa）
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；298 K；Ionic strength (raw mmCIF value) 138.2；Pressure 1
NMR sample composition
200 mM sodium chloride, 20 mM sodium phosphate, 1 mM EDTA, 1 mM PMSF, 5 mM sodium azide, 300 uM [U-100% 13C; U-100% 15N] Grb2-SH2, 90% H2O/10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 6WM1 Crystal structure of the Grb2 SH2 domain in complex with a tripeptide: Ac-pY-Ac6c-N-phenylpropyl Deposited 2020-04-20 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：SH2 Domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；An aqueous solution containing a 1.5 molar ratio of ligand to protein, 10 mg/mL, was prepared. 4.0 ul of this solution was mixed with 3.0 ul precipitant solution containing 0.1 M HEPES, pH 7.5, and 25% w/v polyethylene glycol, MW 10,000, and allowed to equilibrate with 350 ul of the aforementioned precipitant well solution at 298 K. Useable crystals grew after 4 weeks
|
Resolution 1.80 Å R-free 0.245 |
| 6WM1 Crystal structure of the Grb2 SH2 domain in complex with a tripeptide: Ac-pY-Ac6c-N-phenylpropyl Deposited 2020-04-20 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
53–163（111 aa）
Fragment：SH2 Domain
|
Not recorded | GOL GLYCEROL × 2 CA CALCIUM ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；An aqueous solution containing a 1.5 molar ratio of ligand to protein, 10 mg/mL, was prepared. 4.0 ul of this solution was mixed with 3.0 ul precipitant solution containing 0.1 M HEPES, pH 7.5, and 25% w/v polyethylene glycol, MW 10,000, and allowed to equilibrate with 350 ul of the aforementioned precipitant well solution at 298 K. Useable crystals grew after 4 weeks
|
Resolution 1.80 Å R-free 0.245 |
| 6WO2 Crystal Structure of the Grb2 SH2 Domain in Complex with a Tripeptide: Ac-pY-Ac6c-N-isohexyl Deposited 2020-04-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
53–163（111 aa）
Fragment：SH2 Domain
|
Not recorded | CA CALCIUM ION × 1 IPA ISOPROPYL ALCOHOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；An aqueous solution containing a 1.5 molar ratio of ligand to protein, ca. 10 mg/mL, was prepared. 4.0 ul of this solution was mixed with 3.0 ul of a precipitant solution containing 0.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES, and 20% v/v 2-propanol (Hampton crystal screen I, condition no. 27), and allowed to equilibrate with 350 ul of the aforementioned precipitant well solution. Usable crystals grew after 4 weeks
|
Resolution 2.00 Å R-free 0.275 |
| 6WO2 Crystal Structure of the Grb2 SH2 Domain in Complex with a Tripeptide: Ac-pY-Ac6c-N-isohexyl Deposited 2020-04-24 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
53–163（111 aa）
Fragment：SH2 Domain
|
Not recorded | IPA ISOPROPYL ALCOHOL × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；An aqueous solution containing a 1.5 molar ratio of ligand to protein, ca. 10 mg/mL, was prepared. 4.0 ul of this solution was mixed with 3.0 ul of a precipitant solution containing 0.2 M sodium citrate tribasic dihydrate, 0.1 M HEPES, and 20% v/v 2-propanol (Hampton crystal screen I, condition no. 27), and allowed to equilibrate with 350 ul of the aforementioned precipitant well solution. Usable crystals grew after 4 weeks
|
Resolution 2.00 Å R-free 0.275 |
| 7MPH GRB2 SH2 Domain with Compound 7 Deposited 2021-05-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain A
59–152（94 aa）
Chain E
59–152（94 aa）
Chain F
59–152（94 aa）
|
Not recorded | ZLY (4-{(10R,11E,14S,18S)-18-(2-amino-2-oxoethyl)-14-[(naphthalen-1-yl)methyl]-8,17,20-trioxo-7,16,19-triazaspiro[5.14]icos-11-en-10-yl}phenyl)acetic acid × 3 EDO 1,2-ETHANEDIOL × 7 SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；12.4mg/mL GRB2 SH2 domain, 0.1mM Bis-Tris pH 5.5, 2M Ammonium Sulphate
|
Resolution 2.00 Å R-free 0.277 |
| 7MPH GRB2 SH2 Domain with Compound 7 Deposited 2021-05-04 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric |
Chain B
59–152（94 aa）
Chain C
59–152（94 aa）
Chain D
59–152（94 aa）
|
Not recorded | ZLY (4-{(10R,11E,14S,18S)-18-(2-amino-2-oxoethyl)-14-[(naphthalen-1-yl)methyl]-8,17,20-trioxo-7,16,19-triazaspiro[5.14]icos-11-en-10-yl}phenyl)acetic acid × 3 EDO 1,2-ETHANEDIOL × 6 SO4 SULFATE ION × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；291 K；12.4mg/mL GRB2 SH2 domain, 0.1mM Bis-Tris pH 5.5, 2M Ammonium Sulphate
|
Resolution 2.00 Å R-free 0.277 |
| 9I3P CryoEM structure of the Themis:Grb2 complex with bound ProMacrobody 256 Deposited 2025-01-23 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Other combination Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–217（217 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；25 mM Tris pH8, 100 mM NaCl, 2 mM DTT with added 8 mM CHAPSO for cryogrid sample preparation
cryo-EM vitrification conditions
Cryogen ETHANE；Leica EM GP2, 5 s blotting time
|
Resolution 3.30 Å |
| 9IAZ CryoEM structure of the Themis:Grb2 complex with bound ProMacrobody 256, local refinement Deposited 2025-02-11 | Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
1–217（217 aa）
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8；25 mM Tris pH8, 100 mM NaCl, 2 mM DTT with added 8 mM CHAPSO for cryogrid sample preparation
cryo-EM vitrification conditions
Cryogen ETHANE；Leica EM GP2, 5 s blotting time
|
Resolution 3.20 Å |
| 9UOU Crystal structure of the fusion protein of T-lineage protein Themis and adaptor protein Grb2 Deposited 2025-04-26 | Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics | Assembly 1 Insufficient information Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain A
158–214（57 aa）
Chain B
158–214（57 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；289.15 K；0.1 M Tris-HCl pH 8.5, 2% (v/v) Tacsimate pH 8.0, 16% (w/v) polyethylene glycol 3350
|
Resolution 3.06 Å R-free 0.302 |
50 other PDB entries and 96 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | GRB2_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–100； UniProt 54–153 Author chain B； PDBConstruct 1–100； UniProt 54–153 Author chain C； PDBConstruct 1–100； UniProt 54–153 Author chain E； PDBConstruct 1–100； UniProt 54–153 Author chain G； PDBConstruct 1–100； UniProt 54–153 Author chain H； PDBConstruct 1–100； UniProt 54–153 Author chain K； PDBConstruct 1–100； UniProt 54–153 Author chain L； PDBConstruct 1–100； UniProt 54–153 Author chain O； PDBConstruct 1–100； UniProt 54–153 Author chain P； PDBConstruct 1–100； UniProt 54–153 Author chain U； PDBConstruct 1–100； UniProt 54–153 Author chain V； PDBConstruct 1–100； UniProt 54–153 Author chain Y； PDBConstruct 1–100； UniProt 54–153 Author chain Z； PDBConstruct 1–100； UniProt 54–153 Author chain c； PDBConstruct 1–100； UniProt 54–153 Author chain d； PDBConstruct 1–100； UniProt 54–153 |
