Lysine-specific demethylase 4A
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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain A； UniProt 1–359 | Not recorded | ZN ZINC ION × 2 FO2 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound | Resolution 2.21 Å R-free 0.208 |
| 2 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain B； UniProt 1–359 | Not recorded | ZN ZINC ION × 2 FO2 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound | Resolution 2.21 Å R-free 0.208 |
| 3 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain C； UniProt 1–359 | Not recorded | ZN ZINC ION × 2 FO2 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound | Resolution 2.21 Å R-free 0.208 |
| 4 | Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count | Chain D； UniProt 1–359 | Not recorded | ZN ZINC ION × 2 FO2 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 | X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound | Resolution 2.21 Å R-free 0.208 |
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 6H4U | Assembly / Oligomeric State | Construct | Mutations and Modifications | Ligands, Ions and Non-polymers | Method and Experimental Conditions | Structure Quality |
|---|---|---|---|---|---|---|---|
| 2GF7 Double tudor domain structure Deposited 2006-03-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
895–1011（117 aa）
Fragment：double tudor domain
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；1.4 M Ammonium Sulfate, 0.1 M Hepes (7.4), VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 2.20 Å R-free 0.264 |
| 2GF7 Double tudor domain structure Deposited 2006-03-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
895–1011（117 aa）
Fragment：double tudor domain
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；1.4 M Ammonium Sulfate, 0.1 M Hepes (7.4), VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 2.20 Å R-free 0.264 |
| 2GF7 Double tudor domain structure Deposited 2006-03-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
895–1011（117 aa）
Fragment：double tudor domain
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；1.4 M Ammonium Sulfate, 0.1 M Hepes (7.4), VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 2.20 Å R-free 0.264 |
| 2GF7 Double tudor domain structure Deposited 2006-03-21 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
895–1011（117 aa）
Fragment：double tudor domain
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；1.4 M Ammonium Sulfate, 0.1 M Hepes (7.4), VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 2.20 Å R-free 0.264 |
| 2GFA double tudor domain complex structure Deposited 2006-03-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
895–1011（117 aa）
Fragment：double tudor domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；24%PEG 4K, 0.1 M Na Cacodylate (pH 7.4), 0.2 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 2.10 Å R-free 0.270 |
| 2GFA double tudor domain complex structure Deposited 2006-03-21 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
895–1011（117 aa）
Fragment：double tudor domain
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.4；290 K；24%PEG 4K, 0.1 M Na Cacodylate (pH 7.4), 0.2 M Ammonium Sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 290K
|
Resolution 2.10 Å R-free 0.270 |
| 2GP3 Crystal structure of the catalytic core domain of jmjd2a Deposited 2006-04-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–350（349 aa）
|
Not recorded | ZN ZINC ION × 1 FE2 FE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20% PEG8000, 200 mM MgCl2, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.35 Å R-free 0.280 |
| 2GP3 Crystal structure of the catalytic core domain of jmjd2a Deposited 2006-04-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–350（349 aa）
|
Not recorded | ZN ZINC ION × 1 FE2 FE (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20% PEG8000, 200 mM MgCl2, 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.35 Å R-free 0.280 |
| 2GP5 Crystal structure of catalytic core domain of jmjd2A complexed with alpha-Ketoglutarate Deposited 2006-04-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
2–350（349 aa）
|
Not recorded | ZN ZINC ION × 1 FE2 FE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20% PEG 8000, 100 mM MgCl2, 100 Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.28 Å R-free 0.285 |
| 2GP5 Crystal structure of catalytic core domain of jmjd2A complexed with alpha-Ketoglutarate Deposited 2006-04-16 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
2–350（349 aa）
|
Not recorded | ZN ZINC ION × 1 FE2 FE (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；20% PEG 8000, 100 mM MgCl2, 100 Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K
|
Resolution 2.28 Å R-free 0.285 |
| 2OQ6 Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys9 Deposited 2007-01-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；277 K；0.1 M citrate, 4mM NiCl2, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 5.50
|
Resolution 2.00 Å R-free 0.208 |
| 2OQ6 Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys9 Deposited 2007-01-31 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；277 K；0.1 M citrate, 4mM NiCl2, 20% PEG 3350, VAPOR DIFFUSION, SITTING DROP, temperature 277K, pH 5.50
|
Resolution 2.00 Å R-free 0.208 |
| 2OQ7 The crystal structure of JMJD2A complexed with Ni and N-oxalylglycine Deposited 2007-01-31 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 0.1M citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.15 Å R-free 0.228 |
| 2OQ7 The crystal structure of JMJD2A complexed with Ni and N-oxalylglycine Deposited 2007-01-31 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 0.1M citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.15 Å R-free 0.228 |
| 2OS2 Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys36 Deposited 2007-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 0.1 M Citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.30 Å R-free 0.226 |
| 2OS2 Crystal structure of JMJD2A complexed with histone H3 peptide trimethylated at Lys36 Deposited 2007-02-05 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 0.1 M Citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.30 Å R-free 0.226 |
| 2OT7 Crystal structure of JMJD2A complexed with histone H3 peptide monomethylated at Lys9 Deposited 2007-02-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 100 mM Citrate, 2 mM NiCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.13 Å R-free 0.241 |
| 2OT7 Crystal structure of JMJD2A complexed with histone H3 peptide monomethylated at Lys9 Deposited 2007-02-07 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 100 mM Citrate, 2 mM NiCl, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.13 Å R-free 0.241 |
| 2OX0 Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9 Deposited 2007-02-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M Citrate, 4mM NiCl2, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.95 Å R-free 0.210 |
| 2OX0 Crystal structure of JMJD2A complexed with histone H3 peptide dimethylated at Lys9 Deposited 2007-02-19 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M Citrate, 4mM NiCl2, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.95 Å R-free 0.210 |
| 2P5B The complex structure of JMJD2A and trimethylated H3K36 peptide Deposited 2007-03-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–350（349 aa）
Fragment：catalytic core
|
Not recorded | ZN ZINC ION × 1 FE2 FE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 OXY OXYGEN MOLECULE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；EVAPORATION
|
Resolution 1.99 Å R-free 0.263 |
| 2P5B The complex structure of JMJD2A and trimethylated H3K36 peptide Deposited 2007-03-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–350（349 aa）
Fragment：catalytic core
|
Not recorded | ZN ZINC ION × 1 FE2 FE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 OXY OXYGEN MOLECULE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
EVAPORATION；EVAPORATION
|
Resolution 1.99 Å R-free 0.263 |
| 2PXJ The complex structure of JMJD2A and monomethylated H3K36 peptide Deposited 2007-05-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
2–348（347 aa）
Fragment：catalytic core
|
Not recorded | ZN ZINC ION × 1 FE2 FE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；15-17% PEG 5000 mme, pH 8.5, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.00 Å R-free 0.276 |
| 2PXJ The complex structure of JMJD2A and monomethylated H3K36 peptide Deposited 2007-05-14 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
2–348（347 aa）
Fragment：catalytic core
|
Not recorded | ZN ZINC ION × 1 FE2 FE (II) ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 8.5；15-17% PEG 5000 mme, pH 8.5, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.00 Å R-free 0.276 |
| 2Q8C Crystal structure of JMJD2A in ternary complex with an histone H3K9me3 peptide and 2-oxoglutarate Deposited 2007-06-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–350（350 aa）
Fragment：Jumonji domain
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 AKG 2-OXOGLUTARIC ACID × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.05 Å R-free 0.236 |
| 2Q8C Crystal structure of JMJD2A in ternary complex with an histone H3K9me3 peptide and 2-oxoglutarate Deposited 2007-06-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–350（350 aa）
Fragment：Jumonji domain
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 AKG 2-OXOGLUTARIC ACID × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.05 Å R-free 0.236 |
| 2Q8D Crystal structure of JMJ2D2A in ternary complex with histone H3-K36me2 and succinate Deposited 2007-06-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–350（350 aa）
Fragment：Jumonji domain
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 SIN SUCCINIC ACID × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.29 Å R-free 0.251 |
| 2Q8D Crystal structure of JMJ2D2A in ternary complex with histone H3-K36me2 and succinate Deposited 2007-06-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–350（350 aa）
Fragment：Jumonji domain
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 SIN SUCCINIC ACID × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.29 Å R-free 0.251 |
| 2Q8E Specificity and Mechanism of JMJD2A, a Trimethyllysine-Specific Histone Demethylase Deposited 2007-06-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–350（350 aa）
Fragment：Jumonji domain
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 OGA N-OXALYLGLYCINE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.05 Å R-free 0.260 |
| 2Q8E Specificity and Mechanism of JMJD2A, a Trimethyllysine-Specific Histone Demethylase Deposited 2007-06-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–350（350 aa）
Fragment：Jumonji domain
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 OGA N-OXALYLGLYCINE × 1 | X-RAY DIFFRACTION mmCIF provides none of the parsed conditions | Resolution 2.05 Å R-free 0.260 |
| 2QQR JMJD2A hybrid tudor domains Deposited 2007-07-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
897–1011（115 aa）
Fragment：HYBRID TUDOR DOMAINS (Residues: 897-1011)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.213 |
| 2QQR JMJD2A hybrid tudor domains Deposited 2007-07-26 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
897–1011（115 aa）
Fragment：HYBRID TUDOR DOMAINS (Residues: 897-1011)
|
Non-standard monomer：Yes (specific site not provided by mmCIF) | SO4 SULFATE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；2.0 M ammonium sulfate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
|
Resolution 1.80 Å R-free 0.213 |
| 2QQS JMJD2A tandem tudor domains in complex with a trimethylated histone H4-K20 peptide Deposited 2007-07-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
897–1011（115 aa）
Fragment：JMJD2A HYBRID TUDOR DOMAINS (residues: 897-1011)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
293 K；293K
|
Resolution 2.82 Å R-free 0.283 |
| 2QQS JMJD2A tandem tudor domains in complex with a trimethylated histone H4-K20 peptide Deposited 2007-07-26 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
897–1011（115 aa）
Fragment：JMJD2A HYBRID TUDOR DOMAINS (residues: 897-1011)
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
293 K；293K
|
Resolution 2.82 Å R-free 0.283 |
| 2VD7 Crystal Structure of JMJD2A complexed with inhibitor Pyridine-2,4- dicarboxylic acid Deposited 2007-10-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 PD2 PYRIDINE-2,4-DICARBOXYLIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；20% PEG3350 0.1M CITRATE PH 5.5
|
Resolution 2.25 Å R-free 0.219 |
| 2VD7 Crystal Structure of JMJD2A complexed with inhibitor Pyridine-2,4- dicarboxylic acid Deposited 2007-10-01 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 PD2 PYRIDINE-2,4-DICARBOXYLIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；20% PEG3350 0.1M CITRATE PH 5.5
|
Resolution 2.25 Å R-free 0.219 |
| 2WWJ STRUCTURE OF JMJD2A COMPLEXED WITH INHIBITOR 10A Deposited 2009-10-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
7–353（347 aa）
Fragment：RESIDUES 7-353
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 Y28 O-benzyl-N-(carboxycarbonyl)-D-tyrosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；PROTEIN STOCK 11MG/ML JMJD2A, 10MM HEPES PH7.5, 500MM NACL, 5% GLYCEROL, 0.75MM INHIBITOR 10A. RESERVOIR: 0.1M CITRATE PH5.5, 18.5% PEG3350, 4MM NICL2. 1:1 PROTEIN/RESERVOIR
|
Resolution 2.60 Å R-free 0.248 |
| 2WWJ STRUCTURE OF JMJD2A COMPLEXED WITH INHIBITOR 10A Deposited 2009-10-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
7–353（347 aa）
Fragment：RESIDUES 7-353
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 Y28 O-benzyl-N-(carboxycarbonyl)-D-tyrosine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；PROTEIN STOCK 11MG/ML JMJD2A, 10MM HEPES PH7.5, 500MM NACL, 5% GLYCEROL, 0.75MM INHIBITOR 10A. RESERVOIR: 0.1M CITRATE PH5.5, 18.5% PEG3350, 4MM NICL2. 1:1 PROTEIN/RESERVOIR
|
Resolution 2.60 Å R-free 0.248 |
| 2YBK JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE Deposited 2011-03-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 2HG (2R)-2-hydroxypentanedioic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M CITRATE PH 5.5, 4MM NICL2, 20% PEG 3350, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K.
|
Resolution 2.40 Å R-free 0.236 |
| 2YBK JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE Deposited 2011-03-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 2HG (2R)-2-hydroxypentanedioic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M CITRATE PH 5.5, 4MM NICL2, 20% PEG 3350, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K.
|
Resolution 2.40 Å R-free 0.236 |
| 2YBP JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41) Deposited 2011-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–359（359 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1 2HG (2R)-2-hydroxypentanedioic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M CITRATE PH 5.5, 4 MM NICL2, 20% PEG 3350, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K.
|
Resolution 2.02 Å R-free 0.225 |
| 2YBP JMJD2A COMPLEXED WITH R-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41) Deposited 2011-03-09 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–359（359 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 2HG (2R)-2-hydroxypentanedioic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M CITRATE PH 5.5, 4 MM NICL2, 20% PEG 3350, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K.
|
Resolution 2.02 Å R-free 0.225 |
| 2YBS JMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41) Deposited 2011-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–359（359 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 GOL GLYCEROL × 1 S2G (2S)-2-HYDROXYPENTANEDIOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M CITRATE PH 5.5, 4 MM NICL2, 20% PEG 3350, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K.
|
Resolution 2.32 Å R-free 0.237 |
| 2YBS JMJD2A COMPLEXED WITH S-2-HYDROXYGLUTARATE AND HISTONE H3K36me3 PEPTIDE (30-41) Deposited 2011-03-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–359（359 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 S2G (2S)-2-HYDROXYPENTANEDIOIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1 M CITRATE PH 5.5, 4 MM NICL2, 20% PEG 3350, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K.
|
Resolution 2.32 Å R-free 0.237 |
| 3NJY Crystal structure of JMJD2A complexed with 5-carboxy-8-hydroxyquinoline Deposited 2010-06-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：Catalytic domain
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 8XQ 8-hydroxyquinoline-5-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M CITRATE, 4mM NiCl2, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.60 Å R-free 0.226 |
| 3NJY Crystal structure of JMJD2A complexed with 5-carboxy-8-hydroxyquinoline Deposited 2010-06-18 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：Catalytic domain
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 8XQ 8-hydroxyquinoline-5-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M CITRATE, 4mM NiCl2, 20% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.60 Å R-free 0.226 |
| 3PDQ Crystal structure of JMJD2A complexed with bipyridyl inhibitor Deposited 2010-10-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：Catalytic domain, residues 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 KC6 4'-[(2-aminoethyl)carbamoyl]-2,2'-bipyridine-4-carboxylic acid × 1 CL CHLORIDE ION × 4 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M Citrate, 4mM NiCl2, 17.5% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.99 Å R-free 0.207 |
| 3PDQ Crystal structure of JMJD2A complexed with bipyridyl inhibitor Deposited 2010-10-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：Catalytic domain, residues 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 KC6 4'-[(2-aminoethyl)carbamoyl]-2,2'-bipyridine-4-carboxylic acid × 1 CL CHLORIDE ION × 1 NA SODIUM ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M Citrate, 4mM NiCl2, 17.5% PEG 3350, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 1.99 Å R-free 0.207 |
| 3RVH Crystal Structure of JMJD2A Complexed with Inhibitor Deposited 2011-05-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：Catalytic domain
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 HQ2 8-hydroxy-3-(piperazin-1-yl)quinoline-5-carboxylic acid × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M CITRATE, 4mM NiCl2, 20% PEG 3350, 2:1 Protein:Well, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.25 Å R-free 0.224 |
| 3RVH Crystal Structure of JMJD2A Complexed with Inhibitor Deposited 2011-05-06 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：Catalytic domain
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 HQ2 8-hydroxy-3-(piperazin-1-yl)quinoline-5-carboxylic acid × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M CITRATE, 4mM NiCl2, 20% PEG 3350, 2:1 Protein:Well, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.25 Å R-free 0.224 |
| 3U4S Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine Deposited 2011-10-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–359（359 aa）
Fragment：JMJC DOMAIN, UNP residues 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 08P N-(carboxycarbonyl)-D-cysteine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 0.1M citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.15 Å R-free 0.222 |
| 3U4S Histone Lysine demethylase JMJD2A in complex with T11C peptide substrate crosslinked to N-oxalyl-D-cysteine Deposited 2011-10-10 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–359（359 aa）
Fragment：JMJC DOMAIN, UNP residues 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 08P N-(carboxycarbonyl)-D-cysteine × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；20% PEG 3350, 0.1M citrate, 2 mM NiCl2, pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
|
Resolution 2.15 Å R-free 0.222 |
| 4AI9 JMJD2A Complexed with Daminozide Deposited 2012-02-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 DZA DAMINOZIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M CITRATE PH 5.5, 4MM NICL2, 20% PEG 3350, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K
|
Resolution 2.25 Å R-free 0.237 |
| 4AI9 JMJD2A Complexed with Daminozide Deposited 2012-02-08 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 DZA DAMINOZIDE × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.5；277 K；0.1M CITRATE PH 5.5, 4MM NICL2, 20% PEG 3350, VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 277K
|
Resolution 2.25 Å R-free 0.237 |
| 4BIS JMJD2A COMPLEXED WITH 8-HYDROXYQUINOLINE-4-CARBOXYLIC ACID Deposited 2013-04-12 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 8HQ 8-hydroxyquinoline-4-carboxylic acid × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1M BIS-TRIS PROPANE PH 7.5, 0.02M NA/K PHOSPHATE, 20% W/V PEG 3350, SITTING DROP, 277K
|
Resolution 2.49 Å R-free 0.224 |
| 4BIS JMJD2A COMPLEXED WITH 8-HYDROXYQUINOLINE-4-CARBOXYLIC ACID Deposited 2013-04-12 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 8HQ 8-hydroxyquinoline-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；0.1M BIS-TRIS PROPANE PH 7.5, 0.02M NA/K PHOSPHATE, 20% W/V PEG 3350, SITTING DROP, 277K
|
Resolution 2.49 Å R-free 0.224 |
| 4GD4 Crystal Structure of JMJD2A Complexed with Inhibitor Deposited 2012-07-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：catalytic domain
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 0WS 2-(1H-pyrazol-3-yl)pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；277 K；0.2 M NaF, 20% w/v PEG 3350, 0.1 M Bis Tris Propane, pH 7.5, VAPOR DIFFUSION, temperature 277K
|
Resolution 2.33 Å R-free 0.218 |
| 4GD4 Crystal Structure of JMJD2A Complexed with Inhibitor Deposited 2012-07-31 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：catalytic domain
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 3 0WS 2-(1H-pyrazol-3-yl)pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 7.5；277 K；0.2 M NaF, 20% w/v PEG 3350, 0.1 M Bis Tris Propane, pH 7.5, VAPOR DIFFUSION, temperature 277K
|
Resolution 2.33 Å R-free 0.218 |
| 4URA Crystal structure of human JMJD2A in complex with compound 14a Deposited 2014-06-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：RESIDUES 1-359
|
Not recorded | EDO 1,2-ETHANEDIOL × 1 SO4 SULFATE ION × 1 NI NICKEL (II) ION × 1 ZN ZINC ION × 1 LEL 2-(2H-1,2,3-triazol-4-yl)pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350
|
Resolution 2.23 Å R-free 0.259 |
| 4URA Crystal structure of human JMJD2A in complex with compound 14a Deposited 2014-06-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：RESIDUES 1-359
|
Not recorded | SO4 SULFATE ION × 1 NI NICKEL (II) ION × 1 ZN ZINC ION × 1 LEL 2-(2H-1,2,3-triazol-4-yl)pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350
|
Resolution 2.23 Å R-free 0.259 |
| 4V2V JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (25-29) ARK(me3)SA Deposited 2014-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–359（359 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1-359
|
Not recorded | OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；VAPOUR DIFFUSION, SITTING DROP (1:1), 277 K, JCSG/A9: 0.2 M AMMONIUM CHLORIDE, 20 % W/V PEG 3350, pH 7.5
|
Resolution 2.00 Å R-free 0.221 |
| 4V2V JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (25-29) ARK(me3)SA Deposited 2014-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–359（359 aa）
Fragment：CATALYTIC DOMAIN, RESIDUES 1-359
|
Not recorded | OGA N-OXALYLGLYCINE × 1 NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；VAPOUR DIFFUSION, SITTING DROP (1:1), 277 K, JCSG/A9: 0.2 M AMMONIUM CHLORIDE, 20 % W/V PEG 3350, pH 7.5
|
Resolution 2.00 Å R-free 0.221 |
| 4V2W JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35) Deposited 2014-10-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–359（359 aa）
Fragment：CATALYTIC DOMAIN UNP RESIDUES 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；VAPOUR DIFFUSION, SITTING DROP (PROTEIN:WELL, 1:2), 277 K, PACT PREMIER/G10: 0.02 M SODIUM/POTASSIUM PHOSPHATE, 0.1 M BIS TRIS PROPANE 7.5, 20 % W/V PEG 3350
|
Resolution 1.81 Å R-free 0.208 |
| 4V2W JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H3K27me3 PEPTIDE (16-35) Deposited 2014-10-15 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：CATALYTIC DOMAIN UNP RESIDUES 1-359
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；VAPOUR DIFFUSION, SITTING DROP (PROTEIN:WELL, 1:2), 277 K, PACT PREMIER/G10: 0.02 M SODIUM/POTASSIUM PHOSPHATE, 0.1 M BIS TRIS PROPANE 7.5, 20 % W/V PEG 3350
|
Resolution 1.81 Å R-free 0.208 |
| 5A7N Crystal structure of human JMJD2A in complex with compound 43 Deposited 2015-07-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：UNP RESIDUES 1-359
|
Not recorded | MN MANGANESE (II) ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 1 VAO 2-(5-cyano-2-oxidanyl-phenyl)pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；22% PEG3350 -- 0.1M BIS-TRIS PH 7.5 -- 0.25M AMMONIUM SULFATE
|
Resolution 2.39 Å R-free 0.244 |
| 5A7N Crystal structure of human JMJD2A in complex with compound 43 Deposited 2015-07-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：UNP RESIDUES 1-359
|
Not recorded | MN MANGANESE (II) ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 SO4 SULFATE ION × 1 VAO 2-(5-cyano-2-oxidanyl-phenyl)pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 7.5；22% PEG3350 -- 0.1M BIS-TRIS PH 7.5 -- 0.25M AMMONIUM SULFATE
|
Resolution 2.39 Å R-free 0.244 |
| 5A7O Crystal structure of human JMJD2A in complex with compound 42 Deposited 2015-07-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：UNP RESIDUES 1-359
|
Not recorded | SO4 SULFATE ION × 1 7WH 2-[5-(2-methoxyethanoylamino)-2-oxidanyl-phenyl]pyridine-4-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 11 ZN ZINC ION × 1 MN MANGANESE (II) ION × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；PEG3350 -- 0.1M TRIS PH 8.5 -- 0.25M AMMONIUM SULFATE
|
Resolution 2.15 Å R-free 0.222 |
| 5A7O Crystal structure of human JMJD2A in complex with compound 42 Deposited 2015-07-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：UNP RESIDUES 1-359
|
Not recorded | SO4 SULFATE ION × 1 7WH 2-[5-(2-methoxyethanoylamino)-2-oxidanyl-phenyl]pyridine-4-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 5 ZN ZINC ION × 1 MN MANGANESE (II) ION × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；PEG3350 -- 0.1M TRIS PH 8.5 -- 0.25M AMMONIUM SULFATE
|
Resolution 2.15 Å R-free 0.222 |
| 5A7P Crystal structure of human JMJD2A in complex with compound 36 Deposited 2015-07-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：UNP RESIDUES 1-359
|
Not recorded | SO4 SULFATE ION × 1 MN MANGANESE (II) ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 4 6Z1 2-[5-[(5-methyl-1,2-oxazol-3-yl)carbonylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；28% PEG3350, 0.1M BIS-TRIS PH 5.5, 0.15M AMMONIUM SULFATE
|
Resolution 2.28 Å R-free 0.236 |
| 5A7P Crystal structure of human JMJD2A in complex with compound 36 Deposited 2015-07-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：UNP RESIDUES 1-359
|
Not recorded | SO4 SULFATE ION × 1 MN MANGANESE (II) ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 4 6Z1 2-[5-[(5-methyl-1,2-oxazol-3-yl)carbonylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.5；28% PEG3350, 0.1M BIS-TRIS PH 5.5, 0.15M AMMONIUM SULFATE
|
Resolution 2.28 Å R-free 0.236 |
| 5A7Q Crystal structure of human JMJD2A in complex with compound 30 Deposited 2015-07-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：UNP RESIDUES 1-359
|
Not recorded | MN MANGANESE (II) ION × 2 KCH 2-(5-azanyl-2-oxidanyl-phenyl)pyridine-4-carboxylic acid × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；28% PEG3350 -- 0.1M BIS-TRIS PH 6.5 -- 0.15M AMMONIUM SULFATE
|
Resolution 2.00 Å R-free 0.231 |
| 5A7Q Crystal structure of human JMJD2A in complex with compound 30 Deposited 2015-07-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：UNP RESIDUES 1-359
|
Not recorded | MN MANGANESE (II) ION × 2 KCH 2-(5-azanyl-2-oxidanyl-phenyl)pyridine-4-carboxylic acid × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6.5；28% PEG3350 -- 0.1M BIS-TRIS PH 6.5 -- 0.15M AMMONIUM SULFATE
|
Resolution 2.00 Å R-free 0.231 |
| 5A7S Crystal structure of human JMJD2A in complex with compound 44 Deposited 2015-07-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：UNP RESIDUES 1-359
|
Not recorded | MN MANGANESE (II) ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 7 S2X 2-(5-acetamido-2-oxidanyl-phenyl)pyridine-4-carboxylic acid × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；30% PEG3350 -- 0.1M TRIS PH 8.5 -- 0.25M AMMONIUM SULFATE
|
Resolution 2.20 Å R-free 0.228 |
| 5A7S Crystal structure of human JMJD2A in complex with compound 44 Deposited 2015-07-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：UNP RESIDUES 1-359
|
Not recorded | MN MANGANESE (II) ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 8 S2X 2-(5-acetamido-2-oxidanyl-phenyl)pyridine-4-carboxylic acid × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；30% PEG3350 -- 0.1M TRIS PH 8.5 -- 0.25M AMMONIUM SULFATE
|
Resolution 2.20 Å R-free 0.228 |
| 5A7W Crystal structure of human JMJD2A in complex with compound 35 Deposited 2015-07-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：RESIDUES 1-359
|
Not recorded | SO4 SULFATE ION × 1 35M 2-[5-[(4-hydroxyphenyl)carbonylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid × 1 MN MANGANESE (II) ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 2 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；30% PEG3350 -- 0.1M BIS-TRIS PH 6.0 -- 0.25M AMMONIUM SULFATE
|
Resolution 2.27 Å R-free 0.273 |
| 5A7W Crystal structure of human JMJD2A in complex with compound 35 Deposited 2015-07-10 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：RESIDUES 1-359
|
Not recorded | SO4 SULFATE ION × 1 35M 2-[5-[(4-hydroxyphenyl)carbonylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid × 1 MN MANGANESE (II) ION × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；30% PEG3350 -- 0.1M BIS-TRIS PH 6.0 -- 0.25M AMMONIUM SULFATE
|
Resolution 2.27 Å R-free 0.273 |
| 5A80 Crystal structure of human JMJD2A in complex with compound 40 Deposited 2015-07-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：RESIDUES 1-359
|
Not recorded | SO4 SULFATE ION × 1 MN MANGANESE (II) ION × 1 9CJ 2-[5-[2-(3-methoxyphenyl)ethanoylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；30% PEG3350, 0.1M TRIS PH 8.5, 0.2M AMMONIUM SULFATE
|
Resolution 2.28 Å R-free 0.249 |
| 5A80 Crystal structure of human JMJD2A in complex with compound 40 Deposited 2015-07-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：RESIDUES 1-359
|
Not recorded | SO4 SULFATE ION × 1 MN MANGANESE (II) ION × 1 9CJ 2-[5-[2-(3-methoxyphenyl)ethanoylamino]-2-oxidanyl-phenyl]pyridine-4-carboxylic acid × 1 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 8.5；30% PEG3350, 0.1M TRIS PH 8.5, 0.2M AMMONIUM SULFATE
|
Resolution 2.28 Å R-free 0.249 |
| 5ANQ inhibitors of JumonjiC domain-containing histone demethylases Deposited 2015-09-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：JMJN, JMJC, RESIDUES 1-359
|
Not recorded | 5YQ 2-{2-[(pyridin-3-ylmethyl)amino]pyrimidin-4-yl}pyridine-4-carboxylic acid × 1 FE2 FE (II) ION × 1 SO4 SULFATE ION × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.233 M LITHIUM SULFATE, 24% PEG 3350, 0.1 M HEPES PH 7.5
|
Resolution 2.00 Å R-free 0.232 |
| 5ANQ inhibitors of JumonjiC domain-containing histone demethylases Deposited 2015-09-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：JMJN, JMJC, RESIDUES 1-359
|
Not recorded | 5YQ 2-{2-[(pyridin-3-ylmethyl)amino]pyrimidin-4-yl}pyridine-4-carboxylic acid × 1 FE2 FE (II) ION × 1 SO4 SULFATE ION × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
0.233 M LITHIUM SULFATE, 24% PEG 3350, 0.1 M HEPES PH 7.5
|
Resolution 2.00 Å R-free 0.232 |
| 5D6W Crystal structure of double tudor domain of human lysine demethylase KDM4A Deposited 2015-08-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
895–1011（117 aa）
|
Not recorded | SRT S,R MESO-TARTARIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；Protein Solution (30mg/ml KDM4A DTD, 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.0M ammonium tartrate dibasic and 0.1M sodium acetate trihydrate pH4.6) Cryoprotected with additional 20% glycerol
|
Resolution 1.99 Å R-free 0.196 |
| 5D6W Crystal structure of double tudor domain of human lysine demethylase KDM4A Deposited 2015-08-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
895–1011（117 aa）
|
Not recorded | SRT S,R MESO-TARTARIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；Protein Solution (30mg/ml KDM4A DTD, 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.0M ammonium tartrate dibasic and 0.1M sodium acetate trihydrate pH4.6) Cryoprotected with additional 20% glycerol
|
Resolution 1.99 Å R-free 0.196 |
| 5D6W Crystal structure of double tudor domain of human lysine demethylase KDM4A Deposited 2015-08-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
895–1011（117 aa）
|
Not recorded | SRT S,R MESO-TARTARIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；Protein Solution (30mg/ml KDM4A DTD, 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.0M ammonium tartrate dibasic and 0.1M sodium acetate trihydrate pH4.6) Cryoprotected with additional 20% glycerol
|
Resolution 1.99 Å R-free 0.196 |
| 5D6W Crystal structure of double tudor domain of human lysine demethylase KDM4A Deposited 2015-08-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
895–1011（117 aa）
|
Not recorded | SRT S,R MESO-TARTARIC ACID × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 4.6；293 K；Protein Solution (30mg/ml KDM4A DTD, 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.0M ammonium tartrate dibasic and 0.1M sodium acetate trihydrate pH4.6) Cryoprotected with additional 20% glycerol
|
Resolution 1.99 Å R-free 0.196 |
| 5D6X Crystal structure of double tudor domain of human lysine demethylase KDM4A Deposited 2015-08-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
895–1011（117 aa）
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein Solution (30mg/ml KDM4A DTD, 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.0M ammonium sulfate, 1% w/v peg3350 and 0.1M Bis-Tris pH5.5) Cryoprotected with additional 20% glycerol
|
Resolution 2.15 Å R-free 0.200 |
| 5D6X Crystal structure of double tudor domain of human lysine demethylase KDM4A Deposited 2015-08-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
895–1011（117 aa）
|
Not recorded | SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein Solution (30mg/ml KDM4A DTD, 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.0M ammonium sulfate, 1% w/v peg3350 and 0.1M Bis-Tris pH5.5) Cryoprotected with additional 20% glycerol
|
Resolution 2.15 Å R-free 0.200 |
| 5D6Y Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3 Deposited 2015-08-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
895–1011（117 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein-peptide Solution (30mg/ml KDM4A DTD and 3.5mg/ml peptide in 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.2M sodium phosphate monobasic, 0.8M potassium phosphate dibasic, 0.1M CAPS/sodium hydroxide pH10.5, 0.2M lithium sulfate) Cryoprotected with additional 20% glycerol
|
Resolution 2.29 Å R-free 0.295 |
| 5D6Y Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3 Deposited 2015-08-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
895–1011（117 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein-peptide Solution (30mg/ml KDM4A DTD and 3.5mg/ml peptide in 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.2M sodium phosphate monobasic, 0.8M potassium phosphate dibasic, 0.1M CAPS/sodium hydroxide pH10.5, 0.2M lithium sulfate) Cryoprotected with additional 20% glycerol
|
Resolution 2.29 Å R-free 0.295 |
| 5D6Y Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3 Deposited 2015-08-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
895–1011（117 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein-peptide Solution (30mg/ml KDM4A DTD and 3.5mg/ml peptide in 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.2M sodium phosphate monobasic, 0.8M potassium phosphate dibasic, 0.1M CAPS/sodium hydroxide pH10.5, 0.2M lithium sulfate) Cryoprotected with additional 20% glycerol
|
Resolution 2.29 Å R-free 0.295 |
| 5D6Y Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3 Deposited 2015-08-13 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
895–1011（117 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein-peptide Solution (30mg/ml KDM4A DTD and 3.5mg/ml peptide in 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.2M sodium phosphate monobasic, 0.8M potassium phosphate dibasic, 0.1M CAPS/sodium hydroxide pH10.5, 0.2M lithium sulfate) Cryoprotected with additional 20% glycerol
|
Resolution 2.29 Å R-free 0.295 |
| 5D6Y Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3 Deposited 2015-08-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
895–1011（117 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein-peptide Solution (30mg/ml KDM4A DTD and 3.5mg/ml peptide in 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.2M sodium phosphate monobasic, 0.8M potassium phosphate dibasic, 0.1M CAPS/sodium hydroxide pH10.5, 0.2M lithium sulfate) Cryoprotected with additional 20% glycerol
|
Resolution 2.29 Å R-free 0.295 |
| 5D6Y Crystal structure of double tudor domain of human lysine demethylase KDM4A complexed with histone H3K23me3 Deposited 2015-08-13 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
895–1011（117 aa）
|
Not recorded | No recorded non-water small molecule |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；Protein-peptide Solution (30mg/ml KDM4A DTD and 3.5mg/ml peptide in 20mM HEPES pH 7.5, 150mM NaCl and 0.5mM TCEP) mixed in a 1:1 ratio with the well solution (1.2M sodium phosphate monobasic, 0.8M potassium phosphate dibasic, 0.1M CAPS/sodium hydroxide pH10.5, 0.2M lithium sulfate) Cryoprotected with additional 20% glycerol
|
Resolution 2.29 Å R-free 0.295 |
| 5F2S Crystal structure of human KDM4A in complex with compound 15 Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5TZ 2-(2-azanyl-1,3-thiazol-4-yl)pyridine-4-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 7 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.08 Å R-free 0.191 |
| 5F2S Crystal structure of human KDM4A in complex with compound 15 Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5TZ 2-(2-azanyl-1,3-thiazol-4-yl)pyridine-4-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 11 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.08 Å R-free 0.191 |
| 5F2S Crystal structure of human KDM4A in complex with compound 15 Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5TZ 2-(2-azanyl-1,3-thiazol-4-yl)pyridine-4-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 9 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.08 Å R-free 0.191 |
| 5F2S Crystal structure of human KDM4A in complex with compound 15 Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5TZ 2-(2-azanyl-1,3-thiazol-4-yl)pyridine-4-carboxylic acid × 1 EDO 1,2-ETHANEDIOL × 10 DMS DIMETHYL SULFOXIDE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.08 Å R-free 0.191 |
| 5F2W Crystal structure of human KDM4A in complex with compound 16 Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UP 2-(2-azanyl-1,3-thiazol-4-yl)pyridine-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 3 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.60 Å R-free 0.226 |
| 5F2W Crystal structure of human KDM4A in complex with compound 16 Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UP 2-(2-azanyl-1,3-thiazol-4-yl)pyridine-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 10 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.60 Å R-free 0.226 |
| 5F2W Crystal structure of human KDM4A in complex with compound 16 Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UP 2-(2-azanyl-1,3-thiazol-4-yl)pyridine-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.60 Å R-free 0.226 |
| 5F2W Crystal structure of human KDM4A in complex with compound 16 Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UP 2-(2-azanyl-1,3-thiazol-4-yl)pyridine-4-carboxamide × 1 EDO 1,2-ETHANEDIOL × 8 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.60 Å R-free 0.226 |
| 5F32 Crystal structure of human KDM4A in complex with compound 40 Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5V7 8-(2-azanyl-1,3-thiazol-4-yl)-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.05 Å R-free 0.203 |
| 5F32 Crystal structure of human KDM4A in complex with compound 40 Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5V7 8-(2-azanyl-1,3-thiazol-4-yl)-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.05 Å R-free 0.203 |
| 5F32 Crystal structure of human KDM4A in complex with compound 40 Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5V7 8-(2-azanyl-1,3-thiazol-4-yl)-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.05 Å R-free 0.203 |
| 5F32 Crystal structure of human KDM4A in complex with compound 40 Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5V7 8-(2-azanyl-1,3-thiazol-4-yl)-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 EDO 1,2-ETHANEDIOL × 2 GOL GLYCEROL × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.05 Å R-free 0.203 |
| 5F37 Crystal structure of human KDM4A in complex with compound 58 Deposited 2015-12-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：UNP residues 1-359
|
Not recorded | ZN ZINC ION × 2 N5J 3H-pyrido[3,4-d]pyrimidin-4-one × 1 EDO 1,2-ETHANEDIOL × 12 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.22 Å R-free 0.209 |
| 5F37 Crystal structure of human KDM4A in complex with compound 58 Deposited 2015-12-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：UNP residues 1-359
|
Not recorded | ZN ZINC ION × 2 N5J 3H-pyrido[3,4-d]pyrimidin-4-one × 1 EDO 1,2-ETHANEDIOL × 14 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.22 Å R-free 0.209 |
| 5F37 Crystal structure of human KDM4A in complex with compound 58 Deposited 2015-12-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
Fragment：UNP residues 1-359
|
Not recorded | ZN ZINC ION × 2 N5J 3H-pyrido[3,4-d]pyrimidin-4-one × 1 EDO 1,2-ETHANEDIOL × 7 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.22 Å R-free 0.209 |
| 5F37 Crystal structure of human KDM4A in complex with compound 58 Deposited 2015-12-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
Fragment：UNP residues 1-359
|
Not recorded | ZN ZINC ION × 2 N5J 3H-pyrido[3,4-d]pyrimidin-4-one × 1 EDO 1,2-ETHANEDIOL × 10 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.22 Å R-free 0.209 |
| 5F39 Crystal structure of human KDM4A in complex with compound 37 Deposited 2015-12-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：UNP residues 1-359
|
Not recorded | ZN ZINC ION × 2 5UB 8-(1,3-thiazol-4-yl)-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.65 Å R-free 0.210 |
| 5F39 Crystal structure of human KDM4A in complex with compound 37 Deposited 2015-12-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：UNP residues 1-359
|
Not recorded | ZN ZINC ION × 2 5UB 8-(1,3-thiazol-4-yl)-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.65 Å R-free 0.210 |
| 5F39 Crystal structure of human KDM4A in complex with compound 37 Deposited 2015-12-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
Fragment：UNP residues 1-359
|
Not recorded | ZN ZINC ION × 2 5UB 8-(1,3-thiazol-4-yl)-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.65 Å R-free 0.210 |
| 5F39 Crystal structure of human KDM4A in complex with compound 37 Deposited 2015-12-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
Fragment：UNP residues 1-359
|
Not recorded | ZN ZINC ION × 2 5UB 8-(1,3-thiazol-4-yl)-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.65 Å R-free 0.210 |
| 5F3C Crystal structure of human KDM4A in complex with compound 52d Deposited 2015-12-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：UNP residues 1-359
|
Not recorded | ZN ZINC ION × 2 5U8 8-[4-[2-[(4-fluorophenyl)methyl-methyl-amino]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 4 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.06 Å R-free 0.196 |
| 5F3C Crystal structure of human KDM4A in complex with compound 52d Deposited 2015-12-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：UNP residues 1-359
|
Not recorded | ZN ZINC ION × 2 5U8 8-[4-[2-[(4-fluorophenyl)methyl-methyl-amino]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.06 Å R-free 0.196 |
| 5F3C Crystal structure of human KDM4A in complex with compound 52d Deposited 2015-12-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
Fragment：UNP residues 1-359
|
Not recorded | ZN ZINC ION × 2 5U8 8-[4-[2-[(4-fluorophenyl)methyl-methyl-amino]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.06 Å R-free 0.196 |
| 5F3C Crystal structure of human KDM4A in complex with compound 52d Deposited 2015-12-02 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
Fragment：UNP residues 1-359
|
Not recorded | ZN ZINC ION × 2 5U8 8-[4-[2-[(4-fluorophenyl)methyl-methyl-amino]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.06 Å R-free 0.196 |
| 5F3E Crystal structure of human KDM4A in complex with compound 54a Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UO 8-[4-[2-[4-(4-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.16 Å R-free 0.210 |
| 5F3E Crystal structure of human KDM4A in complex with compound 54a Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UO 8-[4-[2-[4-(4-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.16 Å R-free 0.210 |
| 5F3E Crystal structure of human KDM4A in complex with compound 54a Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UO 8-[4-[2-[4-(4-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.16 Å R-free 0.210 |
| 5F3E Crystal structure of human KDM4A in complex with compound 54a Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UO 8-[4-[2-[4-(4-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.16 Å R-free 0.210 |
| 5F3G Crystal structure of human KDM4A in complex with compound 53a Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UL 8-[4-[2-[4-[(4-chlorophenyl)methyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.50 Å R-free 0.246 |
| 5F3G Crystal structure of human KDM4A in complex with compound 53a Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UL 8-[4-[2-[4-[(4-chlorophenyl)methyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.50 Å R-free 0.246 |
| 5F3G Crystal structure of human KDM4A in complex with compound 53a Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UL 8-[4-[2-[4-[(4-chlorophenyl)methyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.50 Å R-free 0.246 |
| 5F3G Crystal structure of human KDM4A in complex with compound 53a Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UL 8-[4-[2-[4-[(4-chlorophenyl)methyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.50 Å R-free 0.246 |
| 5F3I Crystal structure of human KDM4A in complex with compound 54j Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UJ 8-[4-[2-[4-[3,5-bis(chloranyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.24 Å R-free 0.213 |
| 5F3I Crystal structure of human KDM4A in complex with compound 54j Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UJ 8-[4-[2-[4-[3,5-bis(chloranyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.24 Å R-free 0.213 |
| 5F3I Crystal structure of human KDM4A in complex with compound 54j Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UJ 8-[4-[2-[4-[3,5-bis(chloranyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.24 Å R-free 0.213 |
| 5F3I Crystal structure of human KDM4A in complex with compound 54j Deposited 2015-12-02 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 5UJ 8-[4-[2-[4-[3,5-bis(chloranyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.24 Å R-free 0.213 |
| 5F5I Crystal Structure of human JMJD2A complexed with KDOOA011340 Deposited 2015-12-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：Oxidoreductase-2OG
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1 5V1 2-[[(phenylmethyl)amino]methyl]pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.9；277 K；0.1M bis-tris pH 5.9 , 0.15M ammonium sulfate , 13% PEG3350
|
Resolution 2.63 Å R-free 0.243 |
| 5F5I Crystal Structure of human JMJD2A complexed with KDOOA011340 Deposited 2015-12-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：Oxidoreductase-2OG
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 SO4 SULFATE ION × 1 5V1 2-[[(phenylmethyl)amino]methyl]pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 5.9；277 K；0.1M bis-tris pH 5.9 , 0.15M ammonium sulfate , 13% PEG3350
|
Resolution 2.63 Å R-free 0.243 |
| 5FPV Crystal structure of human JMJD2A in complex with compound KDOAM20A Deposited 2015-12-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | MN MANGANESE (II) ION × 1 MMK 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid × 1 ZN ZINC ION × 1 NI NICKEL (II) ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350
|
Resolution 2.44 Å R-free 0.229 |
| 5FPV Crystal structure of human JMJD2A in complex with compound KDOAM20A Deposited 2015-12-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | MN MANGANESE (II) ION × 1 MMK 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid × 1 ZN ZINC ION × 1 NI NICKEL (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350
|
Resolution 2.44 Å R-free 0.229 |
| 5FPV Crystal structure of human JMJD2A in complex with compound KDOAM20A Deposited 2015-12-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | MN MANGANESE (II) ION × 1 MMK 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid × 1 ZN ZINC ION × 1 NI NICKEL (II) ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350
|
Resolution 2.44 Å R-free 0.229 |
| 5FPV Crystal structure of human JMJD2A in complex with compound KDOAM20A Deposited 2015-12-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | MN MANGANESE (II) ION × 1 MMK 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid × 1 ZN ZINC ION × 1 NI NICKEL (II) ION × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350
|
Resolution 2.44 Å R-free 0.229 |
| 5FPV Crystal structure of human JMJD2A in complex with compound KDOAM20A Deposited 2015-12-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 5 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain E
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | MN MANGANESE (II) ION × 1 MMK 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350
|
Resolution 2.44 Å R-free 0.229 |
| 5FPV Crystal structure of human JMJD2A in complex with compound KDOAM20A Deposited 2015-12-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 6 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain F
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | MN MANGANESE (II) ION × 1 MMK 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350
|
Resolution 2.44 Å R-free 0.229 |
| 5FPV Crystal structure of human JMJD2A in complex with compound KDOAM20A Deposited 2015-12-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 7 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain G
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | MN MANGANESE (II) ION × 1 MMK 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid × 1 ZN ZINC ION × 1 NI NICKEL (II) ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350
|
Resolution 2.44 Å R-free 0.229 |
| 5FPV Crystal structure of human JMJD2A in complex with compound KDOAM20A Deposited 2015-12-03 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 8 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain H
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | MN MANGANESE (II) ION × 1 MMK 2-{[(2-{[(E)-2-(dimethylamino)ethenyl](ethyl)amino}-2-oxoethyl)amino]methyl}pyridine-4-carboxylic acid × 1 ZN ZINC ION × 1 NI NICKEL (II) ION × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 5.9；0.1M BIS-TRIS PH 5.9, 0.15M AMMONIUM SULFATE, 11% PEG3350
|
Resolution 2.44 Å R-free 0.229 |
| 5FWE JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE Deposited 2016-02-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–359（359 aa）
Fragment：CATALYTIC DOMAIN
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；SITTING DROPS, 277 K, 0.15 M POTASSIUM BROMIDE, 30 % W/V PEG 2000 MME, pH 7.5
|
Resolution 2.05 Å R-free 0.255 |
| 5FWE JMJD2A COMPLEXED WITH NI(II), NOG AND HISTONE H4(1-15)R3me2s PEPTIDE Deposited 2016-02-15 | Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–359（359 aa）
Fragment：CATALYTIC DOMAIN
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；277 K；SITTING DROPS, 277 K, 0.15 M POTASSIUM BROMIDE, 30 % W/V PEG 2000 MME, pH 7.5
|
Resolution 2.05 Å R-free 0.255 |
| 5FY8 Crystal structure of human JMJD2A in complex with D-threo-isocitrate Deposited 2016-03-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 N81 3-carboxy-2,3-dideoxy-D-erythro-pentaric acid × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.1M BIS-TRIS PH 6.0 -- 0.15M AMMONIUM SULFATE -- 28% PEG3350
|
Resolution 2.34 Å R-free 0.229 |
| 5FY8 Crystal structure of human JMJD2A in complex with D-threo-isocitrate Deposited 2016-03-04 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 N81 3-carboxy-2,3-dideoxy-D-erythro-pentaric acid × 1 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 4 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.1M BIS-TRIS PH 6.0 -- 0.15M AMMONIUM SULFATE -- 28% PEG3350
|
Resolution 2.34 Å R-free 0.229 |
| 5FYC Crystal structure of human JMJD2A in complex with succinate Deposited 2016-03-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 FUM FUMARIC ACID × 1 EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.1M BIS-TRIS PH 6.0 -- 0.15M AMMONIUM SULFATE -- 22% PEG3350
|
Resolution 2.26 Å R-free 0.229 |
| 5FYC Crystal structure of human JMJD2A in complex with succinate Deposited 2016-03-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 FUM FUMARIC ACID × 1 EDO 1,2-ETHANEDIOL × 3 SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.1M BIS-TRIS PH 6.0 -- 0.15M AMMONIUM SULFATE -- 22% PEG3350
|
Resolution 2.26 Å R-free 0.229 |
| 5FYH Crystal structure of human JMJD2A in complex with fumarate Deposited 2016-03-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | ZN ZINC ION × 1 FUM FUMARIC ACID × 1 SO4 SULFATE ION × 1 MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.1M BIS-TRIS PH 6.0 -- 0.15M AMMONIUM SULFATE -- 22% PEG3350
|
Resolution 2.35 Å R-free 0.250 |
| 5FYH Crystal structure of human JMJD2A in complex with fumarate Deposited 2016-03-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | ZN ZINC ION × 1 FUM FUMARIC ACID × 1 SO4 SULFATE ION × 1 MN MANGANESE (II) ION × 1 EDO 1,2-ETHANEDIOL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.1M BIS-TRIS PH 6.0 -- 0.15M AMMONIUM SULFATE -- 22% PEG3350
|
Resolution 2.35 Å R-free 0.250 |
| 5FYI Crystal structure of human JMJD2A in complex with pyruvate Deposited 2016-03-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | NI NICKEL (II) ION × 1 PYR PYRUVIC ACID × 2 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 9 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.1M BIS-TRIS PH 6.0 -- 0.2M AMMONIUM SULFATE -- 28% PEG3350
|
Resolution 2.10 Å R-free 0.236 |
| 5FYI Crystal structure of human JMJD2A in complex with pyruvate Deposited 2016-03-07 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：RESIDUES 4-354
|
Not recorded | NI NICKEL (II) ION × 1 PYR PYRUVIC ACID × 2 DMS DIMETHYL SULFOXIDE × 1 EDO 1,2-ETHANEDIOL × 8 ZN ZINC ION × 1 1KA (2-hydroxyethoxy)acetaldehyde × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
pH 6；0.1M BIS-TRIS PH 6.0 -- 0.2M AMMONIUM SULFATE -- 28% PEG3350
|
Resolution 2.10 Å R-free 0.236 |
| 5LY1 JMJD2A/ KDM4A COMPLEXED WITH NI(II) AND Macrocyclic PEPTIDE Inhibitor CP2 (13-mer) Deposited 2016-09-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric |
Chain A
1–359（359 aa）
Fragment：CATALYTIC DOMAIN UNP residues 1-359
Chain B
1–359（359 aa）
Fragment：CATALYTIC DOMAIN UNP residues 1-359
Chain C
1–359（359 aa）
Fragment：CATALYTIC DOMAIN UNP residues 1-359
Chain D
1–359（359 aa）
Fragment：CATALYTIC DOMAIN UNP residues 1-359
|
Not recorded | NI NICKEL (II) ION × 4 ZN ZINC ION × 4 CL CHLORIDE ION × 3 GOL GLYCEROL × 5 PPI PROPANOIC ACID × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；0.1 M propionate-cacodylate-bistris propane pH 9.0 and 25 % w/v polyethylene glycol 1500
|
Resolution 2.50 Å R-free 0.205 |
| 5LY2 JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Macrocyclic PEPTIDE Inhibitor CP2_R6Kme3 (13-mer) Deposited 2016-09-23 | Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric |
Chain A
1–359（359 aa）
Chain B
1–359（359 aa）
Chain C
1–359（359 aa）
Chain D
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 4 ZN ZINC ION × 4 OGA N-OXALYLGLYCINE × 4 GOL GLYCEROL × 5 CL CHLORIDE ION × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 9；277 K；0.1 M bicine pH 9.0 and 10% w/v polyethylene glycol 6000
|
Resolution 2.43 Å R-free 0.245 |
| 5TVR JMJD2A in complex with Ni(II) and alpha-Ketoglutarate Deposited 2016-11-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：UNP residues 1-159
|
Not recorded | NI NICKEL (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；17.5% PEG-3350 and 0.1 M citrate pH 6.0
|
Resolution 2.09 Å R-free 0.224 |
| 5TVR JMJD2A in complex with Ni(II) and alpha-Ketoglutarate Deposited 2016-11-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：UNP residues 1-159
|
Not recorded | NI NICKEL (II) ION × 1 AKG 2-OXOGLUTARIC ACID × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；17.5% PEG-3350 and 0.1 M citrate pH 6.0
|
Resolution 2.09 Å R-free 0.224 |
| 5TVS JMJD2A in complex with Ni(II) Deposited 2016-11-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：UNP residues 1-159
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；17.5% PEG-3350 and 0.1 M citrate pH 6.0
|
Resolution 2.75 Å R-free 0.267 |
| 5TVS JMJD2A in complex with Ni(II) Deposited 2016-11-09 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：UNP residues 1-159
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 6；277 K；17.5% PEG-3350 and 0.1 M citrate pH 6.0
|
Resolution 2.75 Å R-free 0.267 |
| 5VAR Crystal structure of KDM4A tandem TUDOR domain in complex with a tri-methyl lysine competitive inhibitor Deposited 2017-03-27 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
897–1011（115 aa）
|
Not recorded | 92Y (1R,2S,3R,4S)-3-[(dimethylamino)methyl]-1-phenylbicyclo[2.2.1]heptan-2-ol × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 6.5；290 K；18%(w/v) PEG 8000, 0.2M calcium acetate, 0.1M sodium cacodylate pH 6.5
|
Resolution 1.83 Å R-free 0.243 |
| 5VGI Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 Deposited 2017-04-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 9DJ 3-[({(1R)-6-[methyl(phenyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl}methyl)amino]pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；273 K；25% PEG 4000, 100mM HEPES pH 7.5
|
Resolution 2.07 Å R-free 0.248 |
| 5VGI Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 Deposited 2017-04-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 9DJ 3-[({(1R)-6-[methyl(phenyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl}methyl)amino]pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；273 K；25% PEG 4000, 100mM HEPES pH 7.5
|
Resolution 2.07 Å R-free 0.248 |
| 5VGI Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 Deposited 2017-04-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 9DJ 3-[({(1R)-6-[methyl(phenyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl}methyl)amino]pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；273 K；25% PEG 4000, 100mM HEPES pH 7.5
|
Resolution 2.07 Å R-free 0.248 |
| 5VGI Crystal Structure of KDM4 with the Small Molecule Inhibitor QC6352 Deposited 2017-04-11 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 9DJ 3-[({(1R)-6-[methyl(phenyl)amino]-1,2,3,4-tetrahydronaphthalen-1-yl}methyl)amino]pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；273 K；25% PEG 4000, 100mM HEPES pH 7.5
|
Resolution 2.07 Å R-free 0.248 |
| 5VMP Crystal Structure of Human KDM4 with Small Molecule Inhibitor QC5714 Deposited 2017-04-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 9FJ 3-({[(1R)-6-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]methyl}amino)pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；22% PEG4K, 100mM HEPES pH 7.5
|
Resolution 2.48 Å R-free 0.260 |
| 5VMP Crystal Structure of Human KDM4 with Small Molecule Inhibitor QC5714 Deposited 2017-04-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 9FJ 3-({[(1R)-6-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]methyl}amino)pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；22% PEG4K, 100mM HEPES pH 7.5
|
Resolution 2.48 Å R-free 0.260 |
| 5VMP Crystal Structure of Human KDM4 with Small Molecule Inhibitor QC5714 Deposited 2017-04-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 9FJ 3-({[(1R)-6-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]methyl}amino)pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；22% PEG4K, 100mM HEPES pH 7.5
|
Resolution 2.48 Å R-free 0.260 |
| 5VMP Crystal Structure of Human KDM4 with Small Molecule Inhibitor QC5714 Deposited 2017-04-28 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 9FJ 3-({[(1R)-6-methoxy-1,2,3,4-tetrahydronaphthalen-1-yl]methyl}amino)pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；22% PEG4K, 100mM HEPES pH 7.5
|
Resolution 2.48 Å R-free 0.260 |
| 6CG1 Crystal Structure of KDM4A with Compound 14 Deposited 2018-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 QC1 3-{[(4-fluorophenyl)methyl]amino}pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；20% PEG4K, 150mM NaCl, 50mMHEPES pH 7.3
|
Resolution 2.16 Å R-free 0.240 |
| 6CG1 Crystal Structure of KDM4A with Compound 14 Deposited 2018-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 QC1 3-{[(4-fluorophenyl)methyl]amino}pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；20% PEG4K, 150mM NaCl, 50mMHEPES pH 7.3
|
Resolution 2.16 Å R-free 0.240 |
| 6CG1 Crystal Structure of KDM4A with Compound 14 Deposited 2018-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 QC1 3-{[(4-fluorophenyl)methyl]amino}pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；20% PEG4K, 150mM NaCl, 50mMHEPES pH 7.3
|
Resolution 2.16 Å R-free 0.240 |
| 6CG1 Crystal Structure of KDM4A with Compound 14 Deposited 2018-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 QC1 3-{[(4-fluorophenyl)methyl]amino}pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；293 K；20% PEG4K, 150mM NaCl, 50mMHEPES pH 7.3
|
Resolution 2.16 Å R-free 0.240 |
| 6CG2 Crystal Structure of KDM4A with Compound 8 Deposited 2018-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 QC2 2-[5-(3-hydroxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG4K, 150mM NaCl, 50mM HEPES pH 7.3
|
Resolution 2.34 Å R-free 0.234 |
| 6CG2 Crystal Structure of KDM4A with Compound 8 Deposited 2018-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 QC2 2-[5-(3-hydroxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG4K, 150mM NaCl, 50mM HEPES pH 7.3
|
Resolution 2.34 Å R-free 0.234 |
| 6CG2 Crystal Structure of KDM4A with Compound 8 Deposited 2018-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 QC2 2-[5-(3-hydroxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG4K, 150mM NaCl, 50mM HEPES pH 7.3
|
Resolution 2.34 Å R-free 0.234 |
| 6CG2 Crystal Structure of KDM4A with Compound 8 Deposited 2018-02-19 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
5–354（350 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 QC2 2-[5-(3-hydroxyphenyl)-1H-pyrazol-1-yl]pyridine-4-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；293 K；20% PEG4K, 150mM NaCl, 50mM HEPES pH 7.3
|
Resolution 2.34 Å R-free 0.234 |
| 6G5W Crystal Structure of KDM4A with compound YP-03-038 Deposited 2018-03-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：JMJD2A
|
Not recorded | ZN ZINC ION × 1 NI NICKEL (II) ION × 2 EDO 1,2-ETHANEDIOL × 2 CIT CITRIC ACID × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.5；277 K；100mM Citrate, 10mM NiCl2, 20% PEG 3350
|
Resolution 1.83 Å R-free 0.218 |
| 6G5W Crystal Structure of KDM4A with compound YP-03-038 Deposited 2018-03-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：JMJD2A
|
Not recorded | ZN ZINC ION × 1 NI NICKEL (II) ION × 2 EDO 1,2-ETHANEDIOL × 1 CIT CITRIC ACID × 1 NA SODIUM ION × 1 ENZ (4~{R})-5-methyl-4-phenyl-2-pyridin-2-yl-pyrazolidin-3-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.5；277 K；100mM Citrate, 10mM NiCl2, 20% PEG 3350
|
Resolution 1.83 Å R-free 0.218 |
| 6G5X Crystal Structure of KDM4A with compound YP-02-145 Deposited 2018-03-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
Fragment：JMJD2A
|
Not recorded | ZN ZINC ION × 1 NI NICKEL (II) ION × 3 EDO 1,2-ETHANEDIOL × 2 CIT CITRIC ACID × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.5；277 K；100mM Citrate, 10mM NiCl2, 20% PEG 3350
|
Resolution 1.78 Å R-free 0.203 |
| 6G5X Crystal Structure of KDM4A with compound YP-02-145 Deposited 2018-03-30 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
Fragment：JMJD2A
|
Not recorded | ZN ZINC ION × 1 NI NICKEL (II) ION × 1 EDO 1,2-ETHANEDIOL × 2 CIT CITRIC ACID × 1 MY7 2-(3-methyl-5-oxidanylidene-4-phenyl-4~{H}-pyrazol-1-yl)-3~{H}-benzimidazole-5-carboxylic acid × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 5.5；277 K；100mM Citrate, 10mM NiCl2, 20% PEG 3350
|
Resolution 1.78 Å R-free 0.203 |
| 6H4O Crystal structure of human KDM4A in complex with compound 18a Deposited 2018-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQH 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.25 Å R-free 0.203 |
| 6H4O Crystal structure of human KDM4A in complex with compound 18a Deposited 2018-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQH 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.25 Å R-free 0.203 |
| 6H4O Crystal structure of human KDM4A in complex with compound 18a Deposited 2018-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQH 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.25 Å R-free 0.203 |
| 6H4O Crystal structure of human KDM4A in complex with compound 18a Deposited 2018-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQH 8-[4-[2-[4-[3-(trifluoromethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.25 Å R-free 0.203 |
| 6H4P Crystal structure of human KDM4A in complex with compound 16a Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQ5 8-[4-[2-[4-(3-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 3 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.19 Å R-free 0.207 |
| 6H4P Crystal structure of human KDM4A in complex with compound 16a Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQ5 8-[4-[2-[4-(3-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 CL CHLORIDE ION × 2 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.19 Å R-free 0.207 |
| 6H4P Crystal structure of human KDM4A in complex with compound 16a Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQ5 8-[4-[2-[4-(3-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.19 Å R-free 0.207 |
| 6H4P Crystal structure of human KDM4A in complex with compound 16a Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQ5 8-[4-[2-[4-(3-chlorophenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.19 Å R-free 0.207 |
| 6H4Q Crystal structure of human KDM4A in complex with compound 34a Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FO2 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 GOL GLYCEROL × 2 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.31 Å R-free 0.213 |
| 6H4Q Crystal structure of human KDM4A in complex with compound 34a Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FO2 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.31 Å R-free 0.213 |
| 6H4Q Crystal structure of human KDM4A in complex with compound 34a Deposited 2018-07-23 | Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FO2 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.31 Å R-free 0.213 |
| 6H4Q Crystal structure of human KDM4A in complex with compound 34a Deposited 2018-07-23 | Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FO2 8-[4-(1-methylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.31 Å R-free 0.213 |
| 6H4R Crystal structure of human KDM4A in complex with compound 17f Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQB 8-[4-[2-[4-[4-[2-(dimethylamino)ethyl]phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.14 Å R-free 0.219 |
| 6H4R Crystal structure of human KDM4A in complex with compound 17f Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQB 8-[4-[2-[4-[4-[2-(dimethylamino)ethyl]phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.14 Å R-free 0.219 |
| 6H4R Crystal structure of human KDM4A in complex with compound 17f Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQB 8-[4-[2-[4-[4-[2-(dimethylamino)ethyl]phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.14 Å R-free 0.219 |
| 6H4R Crystal structure of human KDM4A in complex with compound 17f Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQB 8-[4-[2-[4-[4-[2-(dimethylamino)ethyl]phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.14 Å R-free 0.219 |
| 6H4S Crystal structure of human KDM4A in complex with compound 16m Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQE 8-[4-[2-[4-[3-[2-(dimethylamino)ethyl]phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.45 Å R-free 0.218 |
| 6H4S Crystal structure of human KDM4A in complex with compound 16m Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQE 8-[4-[2-[4-[3-[2-(dimethylamino)ethyl]phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.45 Å R-free 0.218 |
| 6H4S Crystal structure of human KDM4A in complex with compound 16m Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQE 8-[4-[2-[4-[3-[2-(dimethylamino)ethyl]phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.45 Å R-free 0.218 |
| 6H4S Crystal structure of human KDM4A in complex with compound 16m Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQE 8-[4-[2-[4-[3-[2-(dimethylamino)ethyl]phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.45 Å R-free 0.218 |
| 6H4T Crystal structure of human KDM4A in complex with compound 19a Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FOW 8-[4-(2-spiro[1,2-dihydroindene-3,4'-piperidine]-1'-ylethyl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.38 Å R-free 0.216 |
| 6H4T Crystal structure of human KDM4A in complex with compound 19a Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FOW 8-[4-(2-spiro[1,2-dihydroindene-3,4'-piperidine]-1'-ylethyl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.38 Å R-free 0.216 |
| 6H4T Crystal structure of human KDM4A in complex with compound 19a Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FOW 8-[4-(2-spiro[1,2-dihydroindene-3,4'-piperidine]-1'-ylethyl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.38 Å R-free 0.216 |
| 6H4T Crystal structure of human KDM4A in complex with compound 19a Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FOW 8-[4-(2-spiro[1,2-dihydroindene-3,4'-piperidine]-1'-ylethyl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 DMS DIMETHYL SULFOXIDE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.38 Å R-free 0.216 |
| 6H4V Crystal structure of human KDM4A in complex with compound 34g Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQN 8-[4-(1-cyclopentylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.15 Å R-free 0.211 |
| 6H4V Crystal structure of human KDM4A in complex with compound 34g Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQN 8-[4-(1-cyclopentylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.15 Å R-free 0.211 |
| 6H4V Crystal structure of human KDM4A in complex with compound 34g Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQN 8-[4-(1-cyclopentylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.15 Å R-free 0.211 |
| 6H4V Crystal structure of human KDM4A in complex with compound 34g Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQN 8-[4-(1-cyclopentylpiperidin-4-yl)pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 DMS DIMETHYL SULFOXIDE × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.15 Å R-free 0.211 |
| 6H4W Crystal structure of human KDM4A in complex with compound 19d Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQQ 8-[4-[2-[4-(3-chlorophenyl)-4-methyl-piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.81 Å R-free 0.266 |
| 6H4W Crystal structure of human KDM4A in complex with compound 19d Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQQ 8-[4-[2-[4-(3-chlorophenyl)-4-methyl-piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.81 Å R-free 0.266 |
| 6H4W Crystal structure of human KDM4A in complex with compound 19d Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQQ 8-[4-[2-[4-(3-chlorophenyl)-4-methyl-piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.81 Å R-free 0.266 |
| 6H4W Crystal structure of human KDM4A in complex with compound 19d Deposited 2018-07-23 | Different ligand/ion Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FQQ 8-[4-[2-[4-(3-chlorophenyl)-4-methyl-piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.81 Å R-free 0.266 |
| 6H4X Crystal structure of human KDM4A in complex with compound 17b Deposited 2018-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FNQ 8-[4-[2-[4-(4-pyridin-3-ylphenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.34 Å R-free 0.207 |
| 6H4X Crystal structure of human KDM4A in complex with compound 17b Deposited 2018-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FNQ 8-[4-[2-[4-(4-pyridin-3-ylphenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.34 Å R-free 0.207 |
| 6H4X Crystal structure of human KDM4A in complex with compound 17b Deposited 2018-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FNQ 8-[4-[2-[4-(4-pyridin-3-ylphenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.34 Å R-free 0.207 |
| 6H4X Crystal structure of human KDM4A in complex with compound 17b Deposited 2018-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FNQ 8-[4-[2-[4-(4-pyridin-3-ylphenyl)piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.34 Å R-free 0.207 |
| 6H4Y Crystal structure of human KDM4A in complex with compound 17e Deposited 2018-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FO8 8-[4-[2-[4-[4-(2-morpholin-4-ylethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.38 Å R-free 0.209 |
| 6H4Y Crystal structure of human KDM4A in complex with compound 17e Deposited 2018-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FO8 8-[4-[2-[4-[4-(2-morpholin-4-ylethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 DMS DIMETHYL SULFOXIDE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.38 Å R-free 0.209 |
| 6H4Y Crystal structure of human KDM4A in complex with compound 17e Deposited 2018-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FO8 8-[4-[2-[4-[4-(2-morpholin-4-ylethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 CL CHLORIDE ION × 1 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.38 Å R-free 0.209 |
| 6H4Y Crystal structure of human KDM4A in complex with compound 17e Deposited 2018-07-23 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 FO8 8-[4-[2-[4-[4-(2-morpholin-4-ylethyl)phenyl]piperidin-1-yl]ethyl]pyrazol-1-yl]-3~{H}-pyrido[3,4-d]pyrimidin-4-one × 1 DMS DIMETHYL SULFOXIDE × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000. Inhibitor is soaked in crystals by addition directly to the drops of DMSO dissolved compound
|
Resolution 2.38 Å R-free 0.209 |
| 6H8P JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer) Deposited 2018-08-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 3 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；277 K；0.1 M MIB buffer (malonic acid/imidazole/boric acid, pH 6.0) 25% w/v polyethylene glycol 1500
|
Resolution 1.98 Å R-free 0.212 |
| 6H8P JMJD2A/ KDM4A COMPLEXED WITH NI(II), NOG AND Histone H1.4(18-32)K26me3 peptide (15-mer) Deposited 2018-08-03 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 CL CHLORIDE ION × 1 OGA N-OXALYLGLYCINE × 1 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION；pH 6；277 K；0.1 M MIB buffer (malonic acid/imidazole/boric acid, pH 6.0) 25% w/v polyethylene glycol 1500
|
Resolution 1.98 Å R-free 0.212 |
| 6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain A
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000.
Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
|
Resolution 2.33 Å R-free 0.280 |
| 6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain B
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000.
Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
|
Resolution 2.33 Å R-free 0.280 |
| 6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain C
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000.
Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
|
Resolution 2.33 Å R-free 0.280 |
| 6HGT Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation Deposited 2018-08-23 | Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric |
Chain D
1–359（359 aa）
|
Not recorded | ZN ZINC ION × 2 OGA N-OXALYLGLYCINE × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；pH 7.5；291 K；Crystallisation solution is 0.1M Bis-Tris-Propane pH7.5, 12-16% PEG-4000.
Co-substrate analog NOG and H3R9 peptide were co-crystallised with the protein.
|
Resolution 2.33 Å R-free 0.280 |
| 7D4A The Crystal Structure of human JMJD2A Tudor domain from Biortus Deposited 2020-09-23 | Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
898–1011（114 aa）
|
Not recorded | SO4 SULFATE ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.1M NaCl, 0.1M HEPES pH7.5, 1.6M (NH4)2SO4
|
Resolution 2.20 Å R-free 0.272 |
| 7EQV Crystal structure of JMJD2A complexed with 3,4-dihydroxybenzoic acid Deposited 2021-05-04 | 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
8–355（348 aa）
|
Not recorded | DHB 3,4-DIHYDROXYBENZOIC ACID × 2 NI NICKEL (II) ION × 2 ZN ZINC ION × 2 CL CHLORIDE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, HANGING DROP；pH 7.5；277 K；15% PEG3350, 0.1 M HEPES pH 7.5, 0.2M NaCl, 277 K, VAPOR DIFFUSION, HANGING DROP
|
Resolution 2.60 Å R-free 0.222 |
| 8WD3 The Crystal Structure of JMJD2A(M1-L359) from Biortus. Deposited 2023-09-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2M KSCN, 0.1M Bis-Tris propane pH7.5, 20% PEG 3350
|
Resolution 3.30 Å R-free 0.293 |
| 8WD3 The Crystal Structure of JMJD2A(M1-L359) from Biortus. Deposited 2023-09-14 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；277 K；0.2M KSCN, 0.1M Bis-Tris propane pH7.5, 20% PEG 3350
|
Resolution 3.30 Å R-free 0.293 |
| 9GII Jumonji domain-containing protein 2A with crystallization epitope mutation R913A Deposited 2024-08-19 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
897–1011（115 aa）
|
Mutation：R913A | SO4 SULFATE ION × 3 GOL GLYCEROL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate,
0.1M bis-tris pH 6.5
|
Resolution 1.70 Å R-free 0.216 |
| 9GLE Jumonji domain-containing protein 2A with crystallization epitope mutations A91T:T93S Deposited 2024-08-27 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 SO4 SULFATE ION × 3 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 5 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M lithium sulfate,
25% PEG3350,
0.1M bis-tris pH 6.5
|
Resolution 1.88 Å R-free 0.222 |
| 9GLE Jumonji domain-containing protein 2A with crystallization epitope mutations A91T:T93S Deposited 2024-08-27 | Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Not recorded | NI NICKEL (II) ION × 1 SO4 SULFATE ION × 2 ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M lithium sulfate,
25% PEG3350,
0.1M bis-tris pH 6.5
|
Resolution 1.88 Å R-free 0.222 |
| 9GP1 Jumonji domain-containing protein 2A with crystallization epitope mutatios K330R:A334E Deposited 2024-09-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
1–359（359 aa）
|
Mutation：R913A | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate,
25% PEG3350,
0.1M bis-tris pH 6.5
|
Resolution 2.21 Å R-free 0.259 |
| 9GP1 Jumonji domain-containing protein 2A with crystallization epitope mutatios K330R:A334E Deposited 2024-09-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain B
1–359（359 aa）
|
Mutation：R913A | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate,
25% PEG3350,
0.1M bis-tris pH 6.5
|
Resolution 2.21 Å R-free 0.259 |
| 9GP1 Jumonji domain-containing protein 2A with crystallization epitope mutatios K330R:A334E Deposited 2024-09-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain C
1–359（359 aa）
|
Mutation：R913A | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate,
25% PEG3350,
0.1M bis-tris pH 6.5
|
Resolution 2.21 Å R-free 0.259 |
| 9GP1 Jumonji domain-containing protein 2A with crystallization epitope mutatios K330R:A334E Deposited 2024-09-06 | Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain D
1–359（359 aa）
|
Mutation：R913A | NI NICKEL (II) ION × 1 ZN ZINC ION × 1 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；0.2M ammonium acetate,
25% PEG3350,
0.1M bis-tris pH 6.5
|
Resolution 2.21 Å R-free 0.259 |
| 9GP4 Jumonji domain-containing protein 2A with crystallization epitope mutations Q953E:A958D Deposited 2024-09-06 | Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics | Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric |
Chain A
897–1011（115 aa）
|
Mutation：Q953E, A958D | EDO 1,2-ETHANEDIOL × 5 SO4 SULFATE ION × 2 |
X-RAY DIFFRACTION
X-ray crystallization conditions
VAPOR DIFFUSION, SITTING DROP；293 K；2M ammonium sulfate,
0.1M bis-tris pH 5.5
|
Resolution 1.59 Å R-free 0.179 |
88 other PDB entries and 233 assemblies. Open the comparison page and filter oligomeric states
View Construct and Data Evidence
| UniProt name | KDM4A_HUMAN |
| Isoform | — |
| PDB entities | 1 |
| Chains and sequence ranges | Author chain A； PDBConstruct 2–360； UniProt 1–359 Author chain B； PDBConstruct 2–360； UniProt 1–359 Author chain C； PDBConstruct 2–360； UniProt 1–359 Author chain D； PDBConstruct 2–360； UniProt 1–359 |
