- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.02 Å
- Oligo State
- monomer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 1 x H0X: [(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]acetonitrile(Non-covalent)
H0X.3: 13 residues within 4Å:- Chain A: R.75, Y.134, A.136, Y.197, F.205, H.208, N.218, K.226, W.228, H.296, N.300
- Ligands: MN.4, DMS.20
9 PLIP interactions:9 interactions with chain A- Hydrophobic interactions: A:Y.134, A:A.136, A:Y.197, A:F.205
- Hydrogen bonds: A:K.226, A:N.300
- Water bridges: A:G.199
- pi-Stacking: A:Y.197, A:F.205
- 2 x MN: MANGANESE (II) ION(Non-covalent)
MN.4: 4 residues within 4Å:- Chain A: H.208, E.210, H.296
- Ligands: H0X.3
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:H.208, A:E.210, A:H.296, H2O.6, H2O.6
MN.5: 3 residues within 4Å:- Chain A: E.387, K.440, R.442
No protein-ligand interaction detected (PLIP)- 1 x CL: CHLORIDE ION(Non-functional Binders)
- 13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.7: 6 residues within 4Å:- Chain A: D.339, C.408, F.409, M.410, S.411
- Ligands: EDO.10
6 PLIP interactions:6 interactions with chain A- Hydrogen bonds: A:D.339, A:F.409, A:M.410, A:S.411, A:S.411
- Water bridges: A:D.339
EDO.8: 8 residues within 4Å:- Chain A: F.60, G.135, A.136, D.137, F.143, L.196, Y.197, V.198
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:G.135, A:V.198
- Water bridges: A:S.140
EDO.9: 5 residues within 4Å:- Chain A: R.375, S.386, L.441, Y.443, T.446
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.375
EDO.10: 6 residues within 4Å:- Chain A: R.321, D.339, M.367, E.371, L.374
- Ligands: EDO.7
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.321, A:D.339, A:E.371
EDO.11: 4 residues within 4Å:- Chain A: P.7, P.276, V.277, Y.278
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:V.277, A:V.277
EDO.12: 8 residues within 4Å:- Chain A: D.397, E.398, R.399, Q.400, V.402, G.420, L.421, L.422
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:D.397, A:Q.400, A:L.422, A:L.422
EDO.13: 3 residues within 4Å:- Chain A: G.233, Y.234, R.293
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.293
EDO.14: 4 residues within 4Å:- Chain A: R.379, V.383, I.384, L.441
No protein-ligand interaction detected (PLIP)EDO.15: 6 residues within 4Å:- Chain A: I.209, W.213, H.326, Y.327, L.330, R.332
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:H.326, A:R.332
- Water bridges: A:W.213, A:E.240, A:R.332
EDO.16: 2 residues within 4Å:- Chain A: L.394, E.398
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:E.398
EDO.17: 4 residues within 4Å:- Chain A: E.387, R.388, M.389, R.442
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.387, A:R.442
EDO.18: 6 residues within 4Å:- Chain A: E.340, K.344, E.392, F.409, R.444, Y.445
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:E.340, A:E.392
- Water bridges: A:E.340
EDO.19: 4 residues within 4Å:- Chain A: R.63, V.76, K.77, D.137
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.63, A:R.63, A:K.77, A:D.137
- 2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.20: 8 residues within 4Å:- Chain A: Q.65, Q.73, T.74, Y.134, S.204, F.205, C.206
- Ligands: H0X.3
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:C.206
DMS.21: 7 residues within 4Å:- Chain A: W.195, Y.197, E.210, S.216, A.308, V.309, N.310
1 PLIP interactions:1 interactions with chain A- Salt bridges: A:E.210
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Nowak, R. et al., Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Mc3960. To be Published
- Release Date
- 2017-03-29
- Peptides
- LYSINE-SPECIFIC DEMETHYLASE 5B: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.02 Å
- Oligo State
- monomer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 1 x H0X: [(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]acetonitrile(Non-covalent)
- 2 x MN: MANGANESE (II) ION(Non-covalent)
- 1 x CL: CHLORIDE ION(Non-functional Binders)
- 13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Nowak, R. et al., Crystal Structure of the Catalytic Domain of Human Jarid1B in Complex with Mc3960. To be Published
- Release Date
- 2017-03-29
- Peptides
- LYSINE-SPECIFIC DEMETHYLASE 5B: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A