- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.39 Å
- Oligo State
- monomer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
DMS.3: 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
DMS.4: 10 residues within 4Å:- Chain A: Q.65, Q.73, T.74, Y.134, S.204, F.205, C.206, V.262
- Ligands: EDO.19, W77.20
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:Q.65
DMS.5: 7 residues within 4Å:- Chain A: I.209, W.213, E.240, R.293, H.326, Y.327, L.330
2 PLIP interactions:2 interactions with chain A- Water bridges: A:Y.327
- Salt bridges: A:E.240
- 1 x MN: MANGANESE (II) ION(Non-covalent)
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.8: 6 residues within 4Å:- Chain A: D.339, C.408, F.409, M.410, S.411
- Ligands: EDO.11
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.9: 7 residues within 4Å:- Chain A: F.60, G.135, A.136, D.137, F.143, L.196, V.198
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:G.135, A:D.137, A:V.198
EDO.10: 5 residues within 4Å:- Chain A: R.375, L.441, Y.443, T.446
- Ligands: EDO.15
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.375
EDO.11: 6 residues within 4Å:- Chain A: R.321, D.339, M.367, E.371, L.374
- Ligands: EDO.8
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.321, A:E.371
- Water bridges: A:D.339, A:D.339
EDO.12: 5 residues within 4Å:- Chain A: P.7, M.271, P.276, V.277, Y.278
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:V.277, A:V.277
EDO.13: 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.14: 3 residues within 4Å:- Chain A: G.233, Y.234, R.293
No protein-ligand interaction detected (PLIP)EDO.15: 5 residues within 4Å:- Chain A: R.379, V.383, I.384, L.441
- Ligands: EDO.10
1 PLIP interactions:1 interactions with chain A- Water bridges: A:R.379
EDO.16: 2 residues within 4Å:- Chain A: H.273, E.274
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:H.273
EDO.17: 9 residues within 4Å:- Chain A: Y.134, G.135, Y.197, V.198, G.199, S.203, S.204, N.300
- Ligands: W77.20
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:S.204, A:N.300
- Water bridges: A:G.199
EDO.18: 3 residues within 4Å:- Chain A: M.243, L.250, L.261
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:L.250
- Water bridges: A:W.207
EDO.19: 5 residues within 4Å:- Chain A: R.75, C.206, H.208
- Ligands: DMS.4, W77.20
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:R.75, A:C.206, A:C.206
- 1 x W77: 2,4-dichloro-N-(pyridin-3-yl)benzamide(Non-covalent)
W77.20: 16 residues within 4Å:- Chain A: R.63, R.75, V.76, K.77, Y.134, A.136, Y.197, S.204, F.205, H.208, W.228, H.296
- Ligands: DMS.4, MN.6, EDO.17, EDO.19
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:Y.134, A:Y.197, A:F.205, A:F.205, A:W.228
- Halogen bonds: A:R.63, A:S.204
- 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 E48115B. To be Published
- Release Date
- 2016-05-04
- Peptides
- LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.39 Å
- Oligo State
- monomer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)
- 1 x MN: MANGANESE (II) ION(Non-covalent)
- 1 x PO4: PHOSPHATE ION(Non-functional Binders)
- 12 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x W77: 2,4-dichloro-N-(pyridin-3-yl)benzamide(Non-covalent)
- 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 E48115B. To be Published
- Release Date
- 2016-05-04
- Peptides
- LYSINE-SPECIFIC DEMETHYLASE 5B, LYSINE-SPECIFIC DEMETHYLASE 5B: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A