Lysine-specific histone demethylase 1A
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 123–852 | Not recorded | REST corepressor 1 × 1 （Q9UKL0） FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 6W1 4-methyl-~{N}-[2-[[4-[[(3~{R})-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 6.5；293 K；The hanging-drop vapor diffusion method at 20 C by mixing equal volumes of 100 microM LSD1-CoREST solution in 5% (w/v) glycerol, 25 mm potassium phosphate, pH 7.2, with reservoir solutions containing 1.2 M sodium/potassium tartrate and 100 mmN-(2-acetamido)-2-iminodiacetic acid, pH 6.5. | Resolution 3.20 Å R-free 0.206 |
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 5LGU | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2COM The solution structure of the SWIRM domain of human LSD1 Deposited 2005-05-18 | Different construct 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
169–279（111 aa）
Fragment：SWIRM domain
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 7；296 K；Ionic strength (raw mmCIF value) 120mM；Pressure ambient
NMR sample composition
1.2mM SWIRM domain U-15N,13C; 20mM d-Tris HCl; 100mM NaCl; 1mM d-DTT; 0.02% NaN3; 10% D2O | 90% H2O/10% D2O
|
Resolution not provided |
| 2DW4 Crystal structure of human LSD1 at 2.3 A resolution Deposited 2006-08-02 | 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
172–831（660 aa）
Fragment：residues 172-831
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；4% PEGMME 2000, 100mM HEPES-Na, 5% MPD, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
|
Resolution 2.30 Å R-free 0.226 |
| 2EJR LSD1-tranylcypromine complex Deposited 2007-03-20 | 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
172–833（662 aa）
Fragment：LSD1, residues 172-833
|
Not recorded | F2N [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-5-[7,8-DIMETHYL-2,4-DIOXO-5-(3-PHENYLPROPANOYL)-1,3,4,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-2,3,4-TRIHYDROXYPENTYL DIHYDROGEN DIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；3.5-4% PEG 2000, 0.1M HEPES-Na, 5% MPD, 5mM Tranylcypromine, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
|
Resolution 2.70 Å R-free 0.245 |
| 2H94 Crystal Structure and Mechanism of human Lysine-Specific Demethylase-1 Deposited 2006-06-08 | 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
172–835（664 aa）
|
Not recorded | HG MERCURY (II) ION × 3 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；9 % PEG 3350
200 mM Diammonium tartrate
100 mM HEPES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
|
Resolution 2.90 Å R-free 0.281 |
| 2HKO Crystal structure of LSD1 Deposited 2006-07-05 | 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
172–835（664 aa）
|
Mutation：R594Q | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.3；289 K；5% PEG 8K, 10 mM MgCl2, 150 mM NaCl, 50 mM Na2HPO4/KH2PO4 pH 6.33, 2mM DTT, VAPOR DIFFUSION, HANGING DROP, temperature 289K, pH 6.30
|
Resolution 2.80 Å R-free 0.283 |
| 2IW5 Structural Basis for CoREST-Dependent Demethylation of Nucleosomes by the Human LSD1 Histone Demethylase Deposited 2006-06-26 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
171–836（666 aa）
Fragment：SWIRM DOMAIN, AMINE OXIDASE DOMAIN AND LINKER, RESIDUES 171-836
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 CL CHLORIDE ION × 3 GOL GLYCEROL × 2 NH4 AMMONIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；VAPOR DIFFUSION, SITTING DROP, 20 DEGREES. DROP: 0.8 MICRO-LITERS OF PROTEIN (10 MG/ML IN 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, 5 MM DTT) PLUS 0.8 MICRO-LITERS OF CRYSTALLIZATION SOLUTION (0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, 10 MM DTT). RESERVOIR: 1 ML OF CRYSTALLIZATION SOLUTION. CRYSTALS APPEARED WITHIN 12 HOURS AND GREW TO THEIR FINAL SIZE WITHIN 10 DAYS. CRYO-PROTECTION SOLUTION: RESERVOIR SOLUTION PLUS 23 PERCENT (V/V) GLYCEROL.
|
Resolution 2.57 Å R-free 0.212 |
| 2L3D The solution structure of the short form SWIRM domain of LSD1 Deposited 2010-09-13 | Different construct 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
174–273（100 aa）
Fragment：SWIRM domain
|
Not recorded | No recorded non-water small molecule |
SOLUTION NMR
NMR measurement conditions
pH 6.5；298 K；Ionic strength (raw mmCIF value) 50；Pressure ambient
NMR sample composition
0.8mM [U-100% 13C; U-100% 15N] SWIRM-1, 50mM sodium phosphate-2, 50mM sodium chloride-3, 2mM DTT-4, 1mM EDTA-5, 90% H2O/10% D2O | 90% H2O/10% D2O
NMR sample composition
0.8mM SWIRM-6, 50mM sodium phosphate-7, 50mM sodium chloride-8, 2mM DTT-9, 1mM EDTA-10, 100% D2O | 100% D2O
|
Resolution not provided |
| 2UXN Structural Basis of Histone Demethylation by LSD1 Revealed by Suicide Inactivation Deposited 2007-03-28 | Different construct 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
171–836（666 aa）
Fragment：SWIRM DOMAIN, AMINE OXIDASE DOMAIN AND LINKER, RESIDUES 171-836
|
Not recorded | FDA DIHYDROFLAVINE-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.6；PROTEIN: 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, AND 5 MM DTT RESERVOIR: 0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, AND 10 MM DTT
|
Resolution 2.72 Å R-free 0.272 |
| 2UXX Human LSD1 Histone Demethylase-CoREST in complex with an FAD- tranylcypromine adduct Deposited 2007-03-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
171–836（666 aa）
Fragment：SWIRM DOMAIN, AMINE OXIDASE DOMAIN AND LINKER, RESIDUES 171-836
|
Not recorded | FAJ FAD-trans-2-Phenylcyclopropylamine Adduct × 1 GOL GLYCEROL × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；VAPOR DIFFUSION, SITTING DROP, 20 DEGREES. DROP: 0.8 MICRO-LITERS OF PROTEIN (10 MG/ML IN 25 MM HEPES, PH 7.4, 200 MM SODIUM CHLORIDE, 1 MM PMSF, 5 MM DTT) PLUS 0.8 MICRO-LITERS OF CRYSTALLIZATION SOLUTION (0.8 M LITHIUM SULFATE, 0.8 M AMMONIUM SULFATE, 0.4 M SODIUM CHLORIDE, 0.1 M SODIUM CITRATE, PH 5.6, 10 MM DTT). RESERVOIR: 1 ML OF CRYSTALLIZATION SOLUTION. CRYSTALS APPEARED WITHIN 12 HOURS AND GREW TO THEIR FINAL SIZE WITHIN 10 DAYS. CRYO-PROTECTION SOLUTION: RESERVOIR SOLUTION PLUS 23 PERCENT (V/V) GLYCEROL.
|
Resolution 2.74 Å R-free 0.260 |
| 2V1D Structural basis of LSD1-CoREST selectivity in histone H3 recognition Deposited 2007-05-23 | Different construct 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
123–852（730 aa）
Fragment：RESIDUES 123-852
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.10 Å R-free 0.239 |
| 2X0L Crystal structure of a neuro-specific splicing variant of human histone lysine demethylase LSD1. Deposited 2009-12-15 | 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
123–852（730 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 3.00 Å R-free 0.252 |
| 2XAF Crystal structure of LSD1-CoREST in complex with para-bromo-(+)-cis-2- phenylcyclopropyl-1-amine Deposited 2010-03-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 TCF 3-(4-BROMOPHENYL)PROPANAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SODIUM/POTASSIUM TARTRATE, ADA BUFFER PH 6.5
|
Resolution 3.25 Å R-free 0.229 |
| 2XAG Crystal structure of LSD1-CoREST in complex with para-bromo-(-)-trans- 2-phenylcyclopropyl-1-amine Deposited 2010-03-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 TCF 3-(4-BROMOPHENYL)PROPANAMIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SODIUM-POTASSIUM TARTRATE, ADA BUFFER PH 6.5
|
Resolution 3.10 Å R-free 0.245 |
| 2XAH Crystal structure of LSD1-CoREST in complex with (+)-trans-2- phenylcyclopropyl-1-amine Deposited 2010-03-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 3PL 3-PHENYLPROPANAL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SODIUM-POTASSIUM TARTRATE, ADA BUFFER PH 6.5
|
Resolution 3.10 Å R-free 0.228 |
| 2XAJ Crystal structure of LSD1-CoREST in complex with (-)-trans-2- phenylcyclopropyl-1-amine Deposited 2010-03-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 TCA PHENYLETHYLENECARBOXYLIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SODIUM-POTASSIUM TARTRATE, ADA BUFFER PH 6.5
|
Resolution 3.30 Å R-free 0.227 |
| 2XAQ Crystal structure of LSD1-CoREST in complex with a tranylcypromine derivative (MC2584, 13b) Deposited 2010-03-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 M84 3-{4-[(PHENYLCARBONYL)AMINO]PHENYL}PROPANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SODIUM-POTASSIUM TARTRATE, ADA BUFFER PH 6.5
|
Resolution 3.20 Å R-free 0.264 |
| 2XAS Crystal structure of LSD1-CoREST in complex with a tranylcypromine derivative (MC2580, 14e) Deposited 2010-03-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 M80 3-[4-({N-[(BENZYLOXY)CARBONYL]-L-PHENYLALANYL}AMINO)PHENYL]PROPANOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
SODIUM-POTASSIUM TARTRATE, ADA BUFFER PH 6.5
|
Resolution 3.20 Å R-free 0.220 |
| 2Y48 Crystal structure of LSD1-CoREST in complex with a N-terminal SNAIL peptide Deposited 2011-01-05 | Different construct 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
123–852（730 aa）
Fragment：RESIDUES 123-852
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
1.2 M SODIUM/POTASSIUM TARTRATE, 100 MM ADA BUFFER PH 6.5
|
Resolution 3.00 Å R-free 0.246 |
| 2Z3Y Crystal structure of Lysine-specific demethylase1 Deposited 2007-06-08 | 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
172–833（662 aa）
Fragment：LSD1, residues 172-833
|
Not recorded | F2N [(2R,3S,4R,5R)-5-(6-AMINO-9H-PURIN-9-YL)-3,4-DIHYDROXYTETRAHYDROFURAN-2-YL]METHYL (2R,3S,4S)-5-[7,8-DIMETHYL-2,4-DIOXO-5-(3-PHENYLPROPANOYL)-1,3,4,5-TETRAHYDROBENZO[G]PTERIDIN-10(2H)-YL]-2,3,4-TRIHYDROXYPENTYL DIHYDROGEN DIPHOSPHATE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1mM Hepes-Na, 5% MPD, 3-4.5% PEG monomethylether 2000, 1mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
|
Resolution 2.25 Å R-free 0.255 |
| 2Z5U Crystal structure of Lysine-specific histone demethylase 1 Deposited 2007-07-17 | 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
172–833（662 aa）
Fragment：LSD1, residues 172-833
|
Not recorded | FAJ FAD-trans-2-Phenylcyclopropylamine Adduct × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；0.1mM Hepes-Na, 5% MPD, 3-4.5% PEG monomethylether 2000, 1mM DTT, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 277.0K
|
Resolution 2.25 Å R-free 0.254 |
| 3ABT Crystal Structure of LSD1 in complex with trans-2-pentafluorophenylcyclopropylamine Deposited 2009-12-21 | 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
172–833（662 aa）
Fragment：amine oxidase (flavin containing) domain 2, residues 172-833
|
Not recorded | 2PF [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-(pentafluorophenyl)-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；3-10% PEG 2000 Monomethyl ether, 0.1M Hepes pH 7.5, 0.2M magnesium chloride, 0.1M cacodylate, 5mM Tranylcypromine-derivative, VAPOR DIFFUSION, HANGING DROP, temperature 278K
|
Resolution 3.20 Å R-free 0.272 |
| 3ABU Crystal Structure of LSD1 in complex with a 2-PCPA derivative, S1201 Deposited 2009-12-21 | 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
172–833（662 aa）
Fragment：amine oxidase (flavin containing) domain 2, residues 172-833
|
Not recorded | 12F [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(1R,3R,3aS)-3-[2-(benzyloxy)-3-fluorophenyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；278 K；3-10% PEG 2000 Monomethyl ether, 0.1M Hepes pH 7.5, 0.2M magnesium chloride, 0.1M cacodylate, 5mM Tranylcypromine-derivative, VAPOR DIFFUSION, HANGING DROP, temperature 278K
|
Resolution 3.10 Å R-free 0.295 |
| 3ZMS LSD1-CoREST in complex with INSM1 peptide Deposited 2013-02-12 | Different construct 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
1–876（876 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 2.96 Å R-free 0.227 |
| 3ZMT LSD1-CoREST in complex with PRSFLV peptide Deposited 2013-02-12 | Different construct 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
1–876（876 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 3.10 Å R-free 0.230 |
| 3ZMU LSD1-CoREST in complex with PKSFLV peptide Deposited 2013-02-12 | Different construct 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
1–876（876 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 3.20 Å R-free 0.226 |
| 3ZMV LSD1-CoREST in complex with PLSFLV peptide Deposited 2013-02-12 | 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 A
1–876（876 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 3.00 Å R-free 0.258 |
| 3ZMZ LSD1-CoREST in complex with PRSFAV peptide Deposited 2013-02-13 | Different construct 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
1–876（876 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 3.00 Å R-free 0.227 |
| 3ZN0 LSD1-CoREST in complex with PRSFAA peptide Deposited 2013-02-13 | Different construct 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
1–876（876 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 2.80 Å R-free 0.244 |
| 3ZN1 LSD1-CoREST in complex with PRLYLV peptide Deposited 2013-02-13 | Different construct 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
1–876（876 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 3.10 Å R-free 0.230 |
| 4BAY Phosphomimetic mutant of LSD1-8a splicing variant in complex with CoREST Deposited 2012-09-17 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
192–876（685 aa）
Fragment：RESIDUES 192-876
|
Mutation：YES | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；20DEG BY HANGING-DROP VAPOR DIFFUSION METHOD BY MIXING EQUAL VOLUMES OF PROTEIN SAMPLES WITH RESERVOIR SOLUTIONS CONTAINING 1.2 M SODIUM/POTASSIUM TARTRATE AND 100 MM N-(2-ACETAMIDO)IMINODIACETIC ACID, PH 6.5
|
Resolution 3.10 Å R-free 0.226 |
| 4CZZ Histone demethylase LSD1(KDM1A)-CoREST3 Complex Deposited 2014-04-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–876（876 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 3.00 Å R-free 0.236 |
| 4KUM Structure of LSD1-CoREST-Tetrahydrofolate complex Deposited 2013-05-22 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
171–836（666 aa）
Fragment：SWIRM andFAD binding domains, residues 171-836
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 1 THG (6S)-5,6,7,8-TETRAHYDROFOLATE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；293 K；0.60 M Li2SO4, 0.63 M (NH4)2SO4, 0.25 M NaCl, 100 mM Na-citrate, pH 5.6, 10 mM DTT, VAPOR DIFFUSION, SITTING DROP, temperature 293K
|
Resolution 3.05 Å R-free 0.217 |
| 4UV8 LSD1(KDM1A)-CoREST in complex with 1-Benzyl-Tranylcypromine Deposited 2014-08-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–876（876 aa）
|
Not recorded | D69 [[(2R,3S,4S)-5-[(4aS,10aS)-4a-[(1S)-3-azanylidene-1,4-diphenyl-butyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-5,10a-dihydro-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentoxy]-oxidanyl-phosphoryl] [(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methyl hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 2.80 Å R-free 0.237 |
| 4UV9 LSD1(KDM1A)-CoREST in complex with 1-Ethyl-Tranylcypromine Deposited 2014-08-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–876（876 aa）
|
Not recorded | D70 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(4aS,10aS)-4a-[(1S,3E)-3-imino-1-phenylpentyl]-7,8-dimethyl-2,4-dioxo-1,3,4,4a,5,10a-hexahydrobenzo[g]pteridin-10(2H)-yl]pentyl dihydrogen diphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PH 6.5
|
Resolution 3.00 Å R-free 0.246 |
| 4UVA LSD1(KDM1A)-CoREST in complex with 1-Methyl-Tranylcypromine (1R,2S) Deposited 2014-08-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–876（876 aa）
|
Not recorded | D73 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(4aS)-4a-[(1S,3E)-3-imino-1-phenylbutyl]-7,8-dimethyl-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]pentyl dihydrogen diphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PH 6.5
|
Resolution 2.90 Å R-free 0.232 |
| 4UVB LSD1(KDM1A)-CoREST in complex with 1-Methyl-Tranylcypromine (1S,2R) Deposited 2014-08-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–876（876 aa）
|
Not recorded | D51 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,7aS)-1-amino-1,10,11-trimethyl-4,6-dioxo-3-phenyl-2,3,5,6,7,7a-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 2.80 Å R-free 0.236 |
| 4UVC LSD1(KDM1A)-CoREST in complex with 1-Phenyl-Tranylcypromine Deposited 2014-08-05 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–876（876 aa）
|
Not recorded | D52 [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-[(1S)-1-azanyl-1,3-diphenyl-propyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-4aH-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；pH 6.5
|
Resolution 3.10 Å R-free 0.241 |
| 4UXN LSD1(KDM1A)-CoREST in complex with Z-Pro derivative of MC2580 Deposited 2014-08-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 M8A benzyl (2R)-2-{[4-(3-oxopropyl)phenyl]carbamoyl}pyrrolidine-1-carboxylate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；PH 6.5
|
Resolution 2.85 Å R-free 0.215 |
| 4XBF Structure of LSD1:CoREST in complex with ssRNA Deposited 2014-12-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–RNA Heteromer；Protein × 8 PDB declaration: dodecameric |
Chain A
171–836（666 aa）
Fragment：UNP residues 171-836
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 4 SO4 SULFATE ION × 20 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.6；290 K；The LSD1-CoREST complex 10-12 mg/ml concentration (in 25 mM HEPES-Na, pH 7.4, 100 mM NaCl, 5 mM DTT, 1 mM PMSF) was mixed (1:1) with the reservoir solution [0.60 M Li2SO4, 0.63 M (NH4)2SO4, 0.25 M NaCl, 100 mM Na-citrate, pH 5.6, 10 mM DTT]
|
Resolution 2.80 Å R-free 0.227 |
| 5AFW Assembly of methylated LSD1 and CHD1 drives AR-dependent transcription and translocation Deposited 2015-01-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
108–119（12 aa）
Fragment：RESIDUES 108-119
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | EDO 1,2-ETHANEDIOL × 9 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.1 M HEPES PH 7.5, 0.2 M L-PROLINE, 10% (W/V) PEG3350
|
Resolution 1.60 Å R-free 0.227 |
| 5H6Q Crystal structure of LSD1-CoREST in complex with peptide 11 Deposited 2016-11-14 | Different construct 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
172–833（662 aa）
Fragment：UNP RESIDUES 172-833
|
Not recorded | GOL GLYCEROL × 4 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(2-Acetamido) iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate.
|
Resolution 2.53 Å R-free 0.247 |
| 5H6R Crystal structure of LSD1-CoREST in complex with peptide 13 Deposited 2016-11-14 | Different construct 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
172–833（662 aa）
Fragment：UNP RESIDUES 172-833
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；293 K；0.1 M N-(2-Acetamido) iminodiacetic acid (pH 5.5), 1.23 M potassium sodium tartrate tetrahydrate
|
Resolution 2.60 Å R-free 0.231 |
| 5IT3 Swirm domain of human Lsd1 Deposited 2016-03-16 | Different construct 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
183–267（85 aa）
Fragment：Swirm domain, UNP residues 183-267
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8.5；293 K；0.1 M MgCl2, 0.1 M Tris, 25%(w/v) PEG 3350
|
Resolution 1.40 Å R-free 0.194 |
| 5IT3 Swirm domain of human Lsd1 Deposited 2016-03-16 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric |
Chain B
183–267（85 aa）
Fragment：Swirm domain, UNP residues 183-267
|
Not recorded | MG MAGNESIUM ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；pH 8.5；293 K；0.1 M MgCl2, 0.1 M Tris, 25%(w/v) PEG 3350
|
Resolution 1.40 Å R-free 0.194 |
| 5L3B Human LSD1/CoREST: LSD1 D556G mutation Deposited 2016-04-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Mutation：D556G | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Tartrate 1-1.4 M, ADA 100 mM pH 6.5
|
Resolution 3.30 Å R-free 0.208 |
| 5L3C Human LSD1/CoREST: LSD1 E379K mutation Deposited 2016-04-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Mutation：E379K | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；Tartrate 1-1.4 M, ADA 100 mM pH 6.5
|
Resolution 3.31 Å R-free 0.223 |
| 5L3D Human LSD1/CoREST: LSD1 Y761H mutation Deposited 2016-04-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；Tartrate 1-1.4 M, ADA 100 mM pH 5.6
|
Resolution 2.60 Å R-free 0.219 |
| 5L3E LSD1-CoREST1 in complex with quinazoline-derivative reversible inhibitor Deposited 2016-04-10 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
123–852（730 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 E11 N~4~-(1-benzylpiperidin-4-yl)-N~2~-[3-(dimethylamino)propyl]-6,7-dimethoxyquinazoline-2,4-diamine × 5 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.3 M Na/K Tartrate, 100 mM ADA
|
Resolution 2.80 Å R-free 0.224 |
| 5L3F LSD1-CoREST1 in complex with polymyxin B Deposited 2016-04-10 | 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
123–852（730 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.3 M Na/K Tartrate
100 mM ADA
|
Resolution 3.50 Å R-free 0.210 |
| 5L3G LSD1-CoREST1 in complex with polymyxin E (colistin) Deposited 2016-04-10 | 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
123–852（730 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NA SODIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.3 M Na/K Tartrate
100 mM ADA
|
Resolution 3.10 Å R-free 0.197 |
| 5LBQ LSD1-CoREST1 in complex with quinazoline-derivative reversible inhibitor Deposited 2016-06-16 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
123–852（730 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 767 N2-(3-(dimethylamino)propyl)-6,7-dimethoxy-N4,N4-dimethylquinazoline-2,4-diamine × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；100 mM ADA pH 6.5
1.2 M Na/Ka Tartrate
|
Resolution 3.30 Å R-free 0.250 |
| 5LGN Thieno[3,2-b]pyrrole-5-carboxamides as Novel Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1: Compound 19 Deposited 2016-07-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
192–860（669 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 6W0 ~{N}-[3-(methoxymethyl)phenyl]-4-methyl-thieno[3,2-b]pyrrole-5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.6；297 K；Sodium Tartrate 1.2 M as precipitant in Sodium Citrate buffer pH 5.6
|
Resolution 3.20 Å R-free 0.220 |
| 5LGT Thieno[3,2-b]pyrrole-5-carboxamides as Novel Reversible Inhibitors of Histone Lysine Demethylase KDM1A/LSD1: Compound 15 Deposited 2016-07-08 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
123–852（730 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 6W3 4-methyl-~{N}-[2-[[4-(1-methylpiperidin-4-yl)oxyphenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；293 K；Hanging-drop vapor diffusion method at 20 C by mixing equal volumes of 100 microM LSD1-CoREST solution in 5% (w/v) glycerol, 25 mm potassium phosphate, pH 7.2, with reservoir solutions containing 1.2 M sodium/potassium tartrate and 100 mmN-(2-acetamido)-2-iminodiacetic acid, pH 6.5.
|
Resolution 3.00 Å R-free 0.230 |
| 5LHG Structure of the KDM1A/CoREST complex with the inhibitor 4-methyl-N-[4-[[4-(1-methylpiperidin-4-yl)oxyphenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide Deposited 2016-07-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 4 6X3 4-methyl-N-[4-[[4-[(1-methyl-4-piperidyl)oxy]phenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.1-1.2 M Na/K tartrate
0.1 M ADA pH 6.0
|
Resolution 3.34 Å R-free 0.192 |
| 5LHH Structure of the KDM1A/CoREST complex with the inhibitor 4-ethyl-N-[3-(methoxymethyl)-2-[[4-[[(3R)-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide Deposited 2016-07-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 6 6X0 4-ethyl-~{N}-[3-(methoxymethyl)-2-[[4-[[(3~{R})-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]thieno[3,2-b]pyrrole-5-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.1-1.2 M Na/K tartrate
0.1 M ADA pH 6.0
|
Resolution 3.05 Å R-free 0.186 |
| 5LHI Structure of the KDM1A/CoREST complex with the inhibitor N-[3-(ethoxymethyl)-2-[[4-[[(3R)-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]-4-methylthieno[3,2-b]pyrrole-5-carboxamide Deposited 2016-07-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 6X5 ~{N}-[3-(ethoxymethyl)-2-[[4-[[(3~{R})-pyrrolidin-3-yl]methoxy]phenoxy]methyl]phenyl]-4-methyl-thieno[3,2-b]pyrrole-5-carboxamide × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.1-1.2 M Na/K tartrate
0.1 M ADA pH 6.0
|
Resolution 3.40 Å R-free 0.225 |
| 5X60 Crystal structure of LSD1-CoREST in complex with peptide 9 Deposited 2017-02-20 | Different construct 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
172–833（662 aa）
Fragment：UNP RESIDUES 172-833
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(2-acetamido)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate.
|
Resolution 2.69 Å R-free 0.236 |
| 5YJB LSD1-CoREST in complex with 4-[5-(piperidin-4-ylmethoxy)-2-(p-tolyl)pyridin-3-yl]benzonitrile Deposited 2017-10-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
172–833（662 aa）
Fragment：UNP residues 172-833
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 8WC 4-[2-(4-methylphenyl)-5-(piperidin-4-ylmethoxy)pyridin-3-yl]benzenecarbonitrile × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M N-(2-ACETAMIDO)IMINODIACETIC ACID (PH 5.5), 1.23M POTASSIUM SODIUM TARTRATE TETRAHYDRATE
|
Resolution 2.96 Å R-free 0.219 |
| 6E1F Crystal structure of the SWIRM domain of human histone lysine-specific demethylase LSD1 Deposited 2018-07-09 | 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
183–267（85 aa）
Fragment：SWIRM domain (UNP residues 183-267)
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Bis-Tris, pH 6.5, 0.1 M potassium chloride, 1.5 M ammonium sulfate
|
Resolution 1.16 Å R-free 0.169 |
| 6E1F Crystal structure of the SWIRM domain of human histone lysine-specific demethylase LSD1 Deposited 2018-07-09 | 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
183–267（85 aa）
Fragment：SWIRM domain (UNP residues 183-267)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Bis-Tris, pH 6.5, 0.1 M potassium chloride, 1.5 M ammonium sulfate
|
Resolution 1.16 Å R-free 0.169 |
| 6E1F Crystal structure of the SWIRM domain of human histone lysine-specific demethylase LSD1 Deposited 2018-07-09 | Different construct 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
183–267（85 aa）
Fragment：SWIRM domain (UNP residues 183-267)
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Bis-Tris, pH 6.5, 0.1 M potassium chloride, 1.5 M ammonium sulfate
|
Resolution 1.16 Å R-free 0.169 |
| 6E1F Crystal structure of the SWIRM domain of human histone lysine-specific demethylase LSD1 Deposited 2018-07-09 | Different construct 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
183–267（85 aa）
Fragment：SWIRM domain (UNP residues 183-267)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M Bis-Tris, pH 6.5, 0.1 M potassium chloride, 1.5 M ammonium sulfate
|
Resolution 1.16 Å R-free 0.169 |
| 6K3E LSD1/Co-Rest structure with an inhibitor Deposited 2019-05-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
172–833（662 aa）
|
Not recorded | CW0 piperidin-4-ylmethyl 4-fluoranyl-4-[[[(1~{R},2~{S})-2-phenylcyclopropyl]amino]methyl]piperidine-1-carboxylate × 1 DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE × 1 ACT ACETATE ION × 2 MLA MALONIC ACID × 3 GOL GLYCEROL × 4 D3U 2-PCPA derivative × 1 EDO 1,2-ETHANEDIOL × 12 PEG DI(HYDROXYETHYL)ETHER × 3 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；291 K；36% Tacsimate
|
Resolution 2.87 Å R-free 0.223 |
| 6KGK LSD1-CoREST-S2101 five-membered ring adduct model Deposited 2019-07-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
172–833（662 aa）
|
Not recorded | GOL GLYCEROL × 3 DJ0 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M N-(carbamoylmethyl)iminodiacetic acid (pH 5.5), 1.23 M potassium sodium tartrate
|
Resolution 2.70 Å R-free 0.206 |
| 6KGL LSD1-CoREST-S2101 N5 adduct model Deposited 2019-07-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
172–833（662 aa）
|
Not recorded | GOL GLYCEROL × 3 DJ0 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M N-(carbamoylmethyl)iminodiacetic acid (pH 5.5), 1.28 M potassium sodium tartrate
|
Resolution 2.70 Å R-free 0.205 |
| 6KGM LSD1-CoREST-S2116 five-membered ring adduct model Deposited 2019-07-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
172–833（662 aa）
|
Not recorded | GOL GLYCEROL × 5 DJ0 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M N-(carbamoylmethyl)iminodiacetic acid (pH 5.5), 1.28 M potassium sodium tartrate
|
Resolution 2.62 Å R-free 0.195 |
| 6KGN LSD1-CoREST-S2116 N5 adduct model Deposited 2019-07-12 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
172–833（662 aa）
|
Not recorded | GOL GLYCEROL × 5 DJ0 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M N-(carbamoylmethyl)iminodiacetic acid (pH 5.5), 1.28 M potassium sodium tartrate
|
Resolution 2.62 Å R-free 0.194 |
| 6KGO LSD1-S2157 five-membered ring adduct model Deposited 2019-07-12 | 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
172–833（662 aa）
|
Not recorded | GOL GLYCEROL × 6 TLA L(+)-TARTARIC ACID × 1 DJ0 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M MES (pH 6.2-6.3), 0.2M diammonium tartrate, 0.0005M TCEP, 10% PEG3350
|
Resolution 2.25 Å R-free 0.204 |
| 6KGP LSD1-S2157 N5 adduct model Deposited 2019-07-12 | 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
172–833（662 aa）
|
Not recorded | GOL GLYCEROL × 6 TLA L(+)-TARTARIC ACID × 1 DJ0 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M MES (pH 6.2-6.3), 0.2M diammonium tartrate, 0.0005M TCEP, 10% PEG3350
|
Resolution 2.25 Å R-free 0.204 |
| 6KGQ LSD1-FCPA-MPE five-membered ring adduct model Deposited 2019-07-12 | 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
172–833（662 aa）
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 DJC 3-[4-[5-fluoranyl-2-(trifluoromethyl)phenyl]phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH 7.5), 5% MPD, 3.5-4.0% PEG MME 2000
|
Resolution 2.32 Å R-free 0.197 |
| 6KGR LSD1-FCPA-MPE N5 adduct model Deposited 2019-07-12 | 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
172–833（662 aa）
|
Not recorded | MPD (4S)-2-METHYL-2,4-PENTANEDIOL × 1 DJC 3-[4-[5-fluoranyl-2-(trifluoromethyl)phenyl]phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M HEPES (pH 7.5), 5% MPD, 3.5-4.0% PEG MME 2000
|
Resolution 2.32 Å R-free 0.198 |
| 6NQM Crystal structure of Human LSD1 Deposited 2019-01-21 | 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
173–830（658 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；296 K；PEG 3350 8%, 0.1 M Ammonium citrate pH6.5
|
Resolution 2.90 Å R-free 0.244 |
| 6NQU Human LSD1 in complex with GSK2879552 Deposited 2019-01-21 | 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
173–830（658 aa）
|
Not recorded | KWM [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[(9~{S},11~{R})-15,16-dimethyl-11-oxidanyl-5,7-bis(oxidanylidene)-9-phenyl-2,4,6,12-tetrazabicyclo[11.4.0]heptadeca-1(17),13,15-trien-2-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7；296 K；PEG3350 6%, 0.1M Ammonium citrate pH7.0
|
Resolution 2.70 Å R-free 0.258 |
| 6NR5 Human LSD1 in complex with Phenelzine sulfate Deposited 2019-01-22 | 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
173–830（658 aa）
|
Not recorded | KXM [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methyl (2R,3R,4R)-5-[(4aR)-7,8-dimethyl-2,4-dioxo-5-(2-phenylethyl)-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；296 K；PEG 3350 95, 0.1M Ammonium citrate pH6.5
|
Resolution 2.90 Å R-free 0.273 |
| 6S35 LSD1/CoREST1 complex with macrocyclic peptide inhibitor Deposited 2019-06-24 | Different construct 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
172–833（662 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.5；295 K；Crystallization: hanging drop, 2 uL total, 1:1 protein-to-reservoir. Protein: 11 mg/mL in 50 mM HEPES, 200 mM NaCl, 2 mM DTT, pH 7.5. Reservoir: 100 mM sodium citrate/citric acid, 1.1 M sodium tartrate, pH 5.5.
Soaking: 100 mM sodium citrate/citric acid, 1.5 M sodium tartrate, 10% glycerol, 1 mM ligand, pH 5.5.
|
Resolution 3.10 Å R-free 0.213 |
| 6TE1 Structure of the KDM1A/CoREST complex with the inhibitor 2-[3-{4-chloro-3-[(4-chlorophenyl)ethynyl]phenyl}-1-(3-morpholin-4-ylpropyl)-1,4,6,7-tetrahydro-5H-pyrazolo[4,3-c]pyridin-5-yl]-2-oxoethanol Deposited 2019-11-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | N4K 5-[4-cyclobutyl-1-[2-(4-piperidin-4-yloxyphenoxy)ethyl]imidazol-2-yl]-4-methyl-thieno[3,2-b]pyrrole × 2 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；293 K；1.1-1.2 M NA/K TARTRATE 0.1 M ADA
|
Resolution 3.11 Å R-free 0.192 |
| 6TUY Human LSD1/CoREST bound to the quinazoline inhibitor MC4106 Deposited 2020-01-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 NY8 ~{N}2-[3-(dimethylamino)propyl]-6,7-dimethoxy-~{N}4-[1-(naphthalen-2-ylmethyl)piperidin-4-yl]quinazoline-2,4-diamine × 3 PO4 PHOSPHATE ION × 1 CL CHLORIDE ION × 5 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；293 K；20 degrees C in 100 mM N-(2-
acetamido)iminodiacetic acid (pH 6.5) and 1.2 M Na-K tartrate
|
Resolution 2.60 Å R-free 0.223 |
| 6VYP Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Deposited 2020-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain K
171–852（682 aa）
Chain M
171–852（682 aa）
|
Mutation：R608A/N717A/D721A Mutation：R608A/N717A/D721A | FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 7.5；277 K；25 mM HEPES pH7.5,
75 mM triammonium citrate,
10% PEG2000-MME,
Modified Microbatch under oil
|
Resolution 4.99 Å R-free 0.277 |
| 6VYP Crystal structure of the LSD1/CoREST histone demethylase bound to its nucleosome substrate Deposited 2020-02-27 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein–DNA Heteromer；Protein × 12 PDB declaration: tetradecameric |
Chain k
171–852（682 aa）
Chain m
171–852（682 aa）
|
Mutation：R608A/N717A/D721A Mutation：R608A/N717A/D721A | FAD FLAVIN-ADENINE DINUCLEOTIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
MICROBATCH；pH 7.5；277 K；25 mM HEPES pH7.5,
75 mM triammonium citrate,
10% PEG2000-MME,
Modified Microbatch under oil
|
Resolution 4.99 Å R-free 0.277 |
| 6W4K Crystal structure of Lysine Specific Demethylase 1 (LSD1) with CC-90011 Deposited 2020-03-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
174–832（659 aa）
|
Not recorded | V0Y 4-[2-(4-aminopiperidin-1-yl)-5-(3-fluoro-4-methoxyphenyl)-1-methyl-6-oxo-1,6-dihydropyrimidin-4-yl]-2-fluorobenzonitrile × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1.3M Na Tartrate
|
Resolution 2.93 Å R-free 0.235 |
| 6WC6 Crystal structure of a truncated LSD1:CoREST in the presence of an LSD1-NT peptide Deposited 2020-03-29 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
171–836（666 aa）
Chain C
137–151（15 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 5.6；298 K；The LSD1-CoREST complex 10mg/ml concentration (in 25 mM HEPES-Na, pH 7.4, 100 mM NaCl, 1 mM TCEP) was mixed (1:1) with the reservoir solution [0.60 M Li2SO4, 0.63 M (NH4)2SO4, 0.25 M NaCl, 100 mM Na-citrate, pH 5.6, 5 mM TCEP]. When get crystals, soak the crystals within 5mM LSD1-NT peptide.
|
Resolution 3.10 Å R-free 0.236 |
| 7CDC Crystal structure of LSD1-CoREST in complex with PRSFLVRRP peptide Deposited 2020-06-19 | Different construct 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
172–833（662 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate
|
Resolution 2.64 Å R-free 0.231 |
| 7CDD Crystal structure of LSD1-CoREST in complex with PRSFLVRR peptide Deposited 2020-06-19 | Different construct 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
172–833（662 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate
|
Resolution 2.76 Å R-free 0.227 |
| 7CDE Crystal structure of LSD1-CoREST in complex with PRSFLVRKR peptide Deposited 2020-06-19 | Different construct 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
172–833（662 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate
|
Resolution 2.68 Å R-free 0.233 |
| 7CDF Crystal structure of LSD1-CoREST in complex with PRSFLVRRK peptide Deposited 2020-06-19 | Different construct 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
172–833（662 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate
|
Resolution 2.68 Å R-free 0.241 |
| 7CDG Crystal structure of LSD1-CoREST in complex with PRSFLVRRR peptide Deposited 2020-06-19 | Different construct 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
172–833（662 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1 M N-(carbamoylmethyl)iminodiacetic acid, 1.23 M potassium sodium tartrate tetrahydrate
|
Resolution 2.80 Å R-free 0.242 |
| 7E0G Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418, FAD-adduct Deposited 2021-01-28 | 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
172–833（662 aa）
|
Not recorded | HUF [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 GOL GLYCEROL × 1 IMD IMIDAZOLE × 2 MG MAGNESIUM ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7；293 K；0.1 M imidazole/HCl (pH 7.0), 14% PEG 3350, 10% 2-methyl-2,4-pentanediol
|
Resolution 2.25 Å R-free 0.238 |
| 7JJL Crystal structure of Importin Alpha 3 in complex with human LSD1 NLS Deposited 2020-07-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
104–129（26 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；0.7 M sodium citrate, 0.01M DTT, 0.1M sodium HEPES pH 7
|
Resolution 2.60 Å R-free 0.266 |
| 7JJM Crystal structure of Importin alpha 2 in complex with LSD1 NLS Deposited 2020-07-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
104–129（26 aa）
|
Not recorded | CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；0.7 M sodium citrate, 0.01M DTT, 0.1M sodium HEPES pH 7
|
Resolution 2.06 Å R-free 0.259 |
| 7JK7 Crystal structure of Importin alpha 2 in complex with LSD1 NLS S111E mutant Deposited 2020-07-27 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
104–129（26 aa）
|
Mutation：S111E | GOL GLYCEROL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；295 K；0.7 M sodium citrate, 0.01M DTT, 0.1M sodium HEPES pH 7
|
Resolution 1.96 Å R-free 0.206 |
| 7VQS Crystal structure of LSD1 in complex with compound 4 Deposited 2021-10-20 | 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
172–833（662 aa）
|
Not recorded | GOL GLYCEROL × 4 TLA L(+)-TARTARIC ACID × 1 7UQ 3-[3,5-bis(fluoranyl)-2-[(2-fluoranylpyridin-3-yl)methoxy]phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M MES (pH 6.2-6.3), 0.2M diammonium tartrate, 0.0005M TCEP, 10-12% PEG 3350
|
Resolution 2.94 Å R-free 0.256 |
| 7VQT Crystal structure of LSD1 in complex with compound 5 Deposited 2021-10-20 | 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
172–833（662 aa）
|
Not recorded | GOL GLYCEROL × 4 TLA L(+)-TARTARIC ACID × 1 7UW 3-[3,5-bis(fluoranyl)-2-[(2-fluoranylpyridin-4-yl)methoxy]phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M MES (pH 6.2-6.3), 0.2M diammonium tartrate, 0.0005M TCEP, 10-12% PEG 3350
|
Resolution 2.91 Å R-free 0.258 |
| 7VQU Crystal structure of LSD1 in complex with compound S1427 Deposited 2021-10-20 | 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
172–833（662 aa）
|
Not recorded | GOL GLYCEROL × 4 TLA L(+)-TARTARIC ACID × 1 7UQ 3-[3,5-bis(fluoranyl)-2-[(2-fluoranylpyridin-3-yl)methoxy]phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M MES (pH 6.2-6.3), 0.2M diammonium tartrate, 0.0005M TCEP, 10-12% PEG 3350
|
Resolution 2.94 Å R-free 0.258 |
| 7W3L Crystal structure of LSD1 in complex with cis-4-Br-2,5-F2-PCPA (S1024) Deposited 2021-11-25 | 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
172–833（662 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 8A2 3-[4-bromanyl-2,5-bis(fluoranyl)phenyl]propanal × 1 TLA L(+)-TARTARIC ACID × 1 GOL GLYCEROL × 6 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；0.1M MES (pH 6.6), 0.2M diammonium tartrate, 0.0005M TCEP, 10-12% PEG 3350
|
Resolution 2.51 Å R-free 0.216 |
| 7XW8 Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAK-418 distomer, FAD-adduct Deposited 2022-05-26 | 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
172–833（662 aa）
|
Not recorded | GOL GLYCEROL × 1 MG MAGNESIUM ION × 2 FA8 [[(2R,3S,4S)-5-[(4AS)-7,8-DIMETHYL-2,4-DIOXO-4A,5-DIHYDROBENZO[G]PTERIDIN-10-YL]-2,3,4-TRIHYDROXY-PENTOXY]-HYDROXY-PHOSPHORYL] [(2R,3S,4R,5R)-5-(6-AMINOPURIN-9-YL)-3,4-DIHYDROXY-OXOLAN-2-YL]METHYL HYDROGEN PHOSPHATE × 1 I00 ~{N}-(oxan-4-yl)-5-(3-oxidanylidenepropyl)thiophene-3-carboxamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；293 K；0.1 M imidazole-HCl (pH 6.5), 10% PEG 3350, 10% 2-methyl-2,4-pentanediol and 50 mM ammonium formate
|
Resolution 2.28 Å R-free 0.230 |
| 8BOP LSD1-CoREST in complex with AW4, long soaking Deposited 2022-11-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | SV9 [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[7,8-dimethyl-2,4-bis(oxidanylidene)-5-[3-[4-(3-phenylphenyl)phenyl]propanoyl]-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.74 Å R-free 0.262 |
| 8BOX LSD1-CoREST in complex with AW4 and SNAG peptide Deposited 2022-11-15 | Different construct 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
1–852（852 aa）
|
Not recorded | SV9 [[(2~{R},3~{S},4~{R},5~{R})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{R},3~{S},4~{S})-5-[7,8-dimethyl-2,4-bis(oxidanylidene)-5-[3-[4-(3-phenylphenyl)phenyl]propanoyl]-1~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.82 Å R-free 0.229 |
| 8F2Z LSD1-CoREST in complex with AW2, short soaking Deposited 2022-11-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | XB3 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-([1,1'-biphenyl]-4-yl)-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 M Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 3.00 Å R-free 0.246 |
| 8F30 LSD1-CoREST in complex with AW2, long soaking Deposited 2022-11-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | XB6 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-{5-[3-([1,1'-biphenyl]-4-yl)propanoyl]-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl}-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 3.10 Å R-free 0.223 |
| 8F59 LSD1-CoREST in complex with AW2 and SNAG peptide Deposited 2022-11-12 | Different construct 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
1–852（852 aa）
|
Not recorded | XB6 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-{5-[3-([1,1'-biphenyl]-4-yl)propanoyl]-7,8-dimethyl-2,4-dioxo-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl}-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.80 Å R-free 0.234 |
| 8F6S LSD1-CoREST in complex with T105 Deposited 2022-11-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | XHT [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2S,3R,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS,13R)-1-hydroxy-10,11-dimethyl-3-{3-[(5-methyl-1,3,4-thiadiazol-2-yl)carbamoyl]phenyl}-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate (non-preferred name) × 1 XHX 3-[(1R,2S)-2-(cyclobutylamino)cyclopropyl]-N-(5-methyl-1,3,4-thiadiazol-2-yl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.91 Å R-free 0.244 |
| 8FDV LSD1-CoREST in complex N-formyl FAD and SNAG peptide Deposited 2022-12-05 | Different construct 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
1–852（852 aa）
|
Not recorded | HUF [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.95 Å R-free 0.252 |
| 8FJ4 LSD1-CoREST in complex with T108, short soaking Deposited 2022-12-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | XZU 3-[(1R,2S)-2-(cyclobutylamino)cyclopropyl]-N-phenylbenzamide × 3 XZQ [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS,13R)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-[3-(phenylcarbamoyl)phenyl]-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.76 Å R-free 0.248 |
| 8FJ7 LSD1-CoREST in complex with T108 and SNAG peptide Deposited 2022-12-19 | Different construct 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
1–852（852 aa）
|
Not recorded | Y0Z [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[7,8-dimethyl-2,4-dioxo-5-{3-[3-(phenylcarbamoyl)phenyl]propanoyl}-1,3,4,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.80 Å R-free 0.243 |
| 8FQJ LSD1-CoREST in complex with T14, short soaking Deposited 2023-01-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | Y66 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2S,3R,4R)-2,3,4-trihydroxy-5-[(1R,3S,3aS,13R)-1-hydroxy-10,11-dimethyl-3-{4-[(5-methyl-1,3,4-thiadiazol-2-yl)carbamoyl]phenyl}-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.90 Å R-free 0.246 |
| 8FRI LSD1-CoREST in complex with AW4, short soaking Deposited 2023-01-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | Y9K [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3S,3aS,13R)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-([1~1~,2~1~:2~3~,3~1~-terphenyl]-1~4~-yl)-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 M Sodium/Potassium Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.80 Å R-free 0.241 |
| 8FRQ LSD1-CoREST in complex with T14, long soaking Deposited 2023-01-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | XF6 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(4aS)-7,8-dimethyl-5-(3-{4-[(5-methyl-1,3,4-thiadiazol-2-yl)carbamoyl]phenyl}propanoyl)-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.89 Å R-free 0.241 |
| 8FRV LSD1-CoREST in complex with T17, short soaking Deposited 2023-01-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | YAF [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-[3-(dimethylcarbamoyl)phenyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；1.2 Sodium/Potassium Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.72 Å R-free 0.248 |
| 8FSK LSD1-CoREST in complex with T18, short soaking Deposited 2023-01-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | YAO [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-(3-benzamidophenyl)-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Sodium/Potassium Tartrate, 100 mM ADA pH 6.5
|
Resolution 3.13 Å R-free 0.223 |
| 8GJ6 LSD1-CoREST in complex with T16 Deposited 2023-03-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | ZSI [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3S,3aS,13R)-1-hydroxy-10,11-dimethyl-3-[3-(methylcarbamoyl)phenyl]-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate (non-preferred name) × 1 K POTASSIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Sodium/Potassium Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.77 Å R-free 0.251 |
| 8INL LSD1 in complex with S2172 Deposited 2023-03-10 | 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
172–833（662 aa）
|
Not recorded | TLA L(+)-TARTARIC ACID × 1 GOL GLYCEROL × 5 DJ0 3-[3,5-bis(fluoranyl)-2-phenylmethoxy-phenyl]propanal × 1 FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；0.1M MES (pH 6.5), 0.2M diammonium tartrate, 0.0005M TCEP, 14% PEG 3350
|
Resolution 2.62 Å R-free 0.216 |
| 8JF5 Crystal structure of Lysine Specific Demethylase 1 (LSD1) with TAS1440 Deposited 2023-05-17 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
172–833（662 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 UEU 4-[5-[(3~{R})-3-azanylpyrrolidin-1-yl]carbonyl-2-[2-fluoranyl-4-(2-methyl-2-oxidanyl-propyl)phenyl]phenyl]-2-fluoranyl-benzenecarbonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；293 K；100mM ADA pH6.5, 1.22M Na/K Tartrate
|
Resolution 3.20 Å R-free 0.230 |
| 8Q1G LSD1-CoREST bound to Acetylated K14 of Histone H3 Deposited 2023-07-31 | 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
123–852（730 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartrate 1.2M, ADA 0.1M,
|
Resolution 2.60 Å R-free 0.255 |
| 8Q1H LSD1 Y391K-CoREST bound to Histone H3 N-terminal tail Deposited 2023-07-31 | 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
123–852（730 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartrate 1.2 M, ADA 0.1M
|
Resolution 2.90 Å R-free 0.254 |
| 8Q1J LSD1 Y391K-CoREST bound to Acetylated K14 of Histone H3 Deposited 2023-07-31 | 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
123–852（730 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；Sodium Tartate 1.2 M, ADA 0.1M
|
Resolution 2.87 Å R-free 0.272 |
| 8UL6 LSD1-CoREST in complex with T16, long soaking Deposited 2023-10-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | ZSI [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3S,3aS,13R)-1-hydroxy-10,11-dimethyl-3-[3-(methylcarbamoyl)phenyl]-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 Sodium Potassium Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.74 Å R-free 0.241 |
| 8UL8 LSD1-CoREST in complex with T15, short soaking Deposited 2023-10-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | XRK methyl 3-{(1R,3S,3aS,13R)-8-[(2S,3S,4R)-5-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-2,3,4-trihydroxypentyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,4,5,6,8-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-3-yl}benzoate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.82 Å R-free 0.247 |
| 8ULB LSD1-CoREST in complex with T17, long soaking Deposited 2023-10-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | YAF [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-[3-(dimethylcarbamoyl)phenyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.2 M Sodium Potassium Tartrate, 100 mM ADA pH 6.5
|
Resolution 3.41 Å R-free 0.216 |
| 8ULC LSD1-CoREST in complex with T15, long soaking Deposited 2023-10-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | XRK methyl 3-{(1R,3S,3aS,13R)-8-[(2S,3S,4R)-5-{[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}-2,3,4-trihydroxypentyl]-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,4,5,6,8-hexahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-3-yl}benzoate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.2 M Sodium Potassium Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.82 Å R-free 0.255 |
| 8ULZ LSD1-CoREST in complex with T18 and SNAG peptide Deposited 2023-10-17 | Different construct 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
1–852（852 aa）
|
Not recorded | YAO [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-(3-benzamidophenyl)-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.2 Sodium Potassium Tartrate, 100 mM ADA pH 6.5
|
Resolution 3.32 Å R-free 0.231 |
| 8UMQ LSD1-CoREST in complex with T18, long soaking Deposited 2023-10-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | YAO [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-5-[(1R,3S,3aS,13R)-3-(3-benzamidophenyl)-1-hydroxy-10,11-dimethyl-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.2 Sodium Potassium Tartrate, 100 mM ADA pH 6.5
|
Resolution 3.26 Å R-free 0.209 |
| 8UNI LSD1-CoREST with N-formyl-FAD in complex with H3K4M histone tail Deposited 2023-10-19 | Different construct 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
1–852（852 aa）
|
Not recorded | HUF [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.2 M Sodium Potassium Tartrate, 100 mM ADA pH 6.5
|
Resolution 3.40 Å R-free 0.252 |
| 8UOM LSD1-CoREST with N-formyl-FAD in complex with H3dimeK4 histone tail Deposited 2023-10-20 | Different construct 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
1–852（852 aa）
|
Not recorded | HUF [[(2R,3S,4R,5R)-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2R,3S,4S)-5-[5-methanoyl-7,8-dimethyl-2,4-bis(oxidanylidene)-1H-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 3.20 Å R-free 0.240 |
| 8YM7 Crystal structure of Lysine Specific Demethylase 1 (LSD1) with JH-45 Deposited 2024-03-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
173–832（660 aa）
|
Not recorded | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 A1LZJ 4-[5-(4-azanylpiperidin-1-yl)-8-(4-methylphenyl)pyrido[3,4-b]pyrazin-7-yl]-2-fluoranyl-benzenecarbonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Sodium acetate pH 4.6
1.2 M Sodium malonate
|
Resolution 2.83 Å R-free 0.248 |
| 9DBP Crystal structure of the LSD1/CoREST histone demethylase in complex with the cofactor FAD and the inhibitor GSK690 Deposited 2024-08-23 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
172–831（660 aa）
|
Mutation：R269A,K469A | FAD FLAVIN-ADENINE DINUCLEOTIDE × 1 GOL GLYCEROL × 2 A1A5U 4-[2-(4-methylphenyl)-5-{[(3R)-pyrrolidin-3-yl]methoxy}pyridin-3-yl]benzonitrile × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；100 mM ADA, 1.2 - 1.6M N/K and 3% w/v D-(+)-Glucose monohydrate
|
Resolution 2.66 Å R-free 0.250 |
| 9DWU CoREST complex bound to U2AF2 Deposited 2024-10-10 | Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric |
Chain A
171–836（666 aa）
Fragment：UNP residues 171-836
|
Not recorded | No recorded non-water small molecule |
ELECTRON MICROSCOPY
cryo-EM buffer
pH 8
cryo-EM vitrification conditions
Cryogen ETHANE
|
Resolution 5.14 Å |
| 9EL7 LSD1-CoREST in complex with T105 enantiomer (1R,2S) Deposited 2024-12-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | A1BI4 [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2S,3S,4R)-5-[(4aS)-7,8-dimethyl-4a-[(1R)-1-{3-[(5-methyl-1,3,4-thiadiazol-2-yl)carbamoyl]phenyl}-3-oxopropyl]-2,4-dioxo-3,4,4a,5-tetrahydrobenzo[g]pteridin-10(2H)-yl]-2,3,4-trihydroxypentyl dihydrogen diphosphate (non-preferred name) × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；300 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.87 Å R-free 0.242 |
| 9EL8 LSD1-CoREST in complex with T105 1S2R enantiomer Deposited 2024-12-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | XHT [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2S,3R,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS,13R)-1-hydroxy-10,11-dimethyl-3-{3-[(5-methyl-1,3,4-thiadiazol-2-yl)carbamoyl]phenyl}-4,6-dioxo-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate (non-preferred name) × 1 XHX 3-[(1R,2S)-2-(cyclobutylamino)cyclopropyl]-N-(5-methyl-1,3,4-thiadiazol-2-yl)benzamide × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；300 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.91 Å R-free 0.244 |
| 9ELA LSD1-CoREST in complex with T108, long soaking Deposited 2024-12-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | XZQ [(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxyoxolan-2-yl]methyl (2R,3S,4S)-2,3,4-trihydroxy-5-[(1R,3R,3aS,13R)-1-hydroxy-10,11-dimethyl-4,6-dioxo-3-[3-(phenylcarbamoyl)phenyl]-2,3,5,6-tetrahydro-1H-benzo[g]pyrrolo[2,1-e]pteridin-8(4H)-yl]pentyl dihydrogen diphosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；300 K；1.2 Na/K Tartrate, 100 mM ADA pH 6.5
|
Resolution 2.85 Å R-free 0.243 |
| 9F0A N5 Adduct of LSD1-CoREST in complex with MC4455 Deposited 2024-04-15 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
123–852（730 aa）
|
Not recorded | A1H8N [[(2~{S},3~{R},4~{S},5~{S})-5-(6-aminopurin-9-yl)-3,4-bis(oxidanyl)oxolan-2-yl]methoxy-oxidanyl-phosphoryl] [(2~{S},3~{S},4~{R})-5-[5-[3-[4-[[4-[[(2~{S})-3-(3,4-dihydro-1~{H}-isoquinolin-2-yl)-2-oxidanyl-propyl]carbamoyl]pyridin-2-yl]amino]phenyl]propanoyl]-7,8-dimethyl-2,4-bis(oxidanylidene)-4~{a}~{H}-benzo[g]pteridin-10-yl]-2,3,4-tris(oxidanyl)pentyl] hydrogen phosphate × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6.5；293 K；1.2 M Sodium Tartrate, 0.1 M ADA, pH 6.5
|
Resolution 3.36 Å R-free 0.234 |
| 9FWG LSD1/CoREST bound to bomedemstat Deposited 2024-06-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–852（852 aa）
|
Not recorded | A1IG2 Bomedemstat FAD adduct × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6.5；293 K；100 mM N-(2-Acetamido)iminodiacetic acid (ADA) pH 6.5, 1.2 M Na/K Tartrate. Crystals were soaked in a solution containing 1 mM bomedemstat for 2 hours at 20 degress
|
Resolution 3.20 Å R-free 0.227 |
126 other PDB entries and 131 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | KDM1A_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 1–730； UniProt 123–852 |
