- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.05 Å
- Oligo State
- monomer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 1 x MN: MANGANESE (II) ION(Non-covalent)
- 1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)
EPE.4: 14 residues within 4Å:- Chain A: I.209, W.213, E.240, M.243, L.250, F.251, L.261, V.262, R.293, Y.295, H.326, Y.327, L.330, R.332
7 PLIP interactions:7 interactions with chain A- Hydrogen bonds: A:W.207
- Water bridges: A:R.332
- Salt bridges: A:E.240, A:R.293, A:H.326, A:R.332
- pi-Cation interactions: A:F.251
- 13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.5: 6 residues within 4Å:- Chain A: D.339, C.408, F.409, M.410, S.411
- Ligands: EDO.8
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:D.339, A:F.409, A:M.410, A:S.411, A:S.411
EDO.6: 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.7: 6 residues within 4Å:- Chain A: R.375, S.386, L.441, Y.443, T.446
- Ligands: EDO.12
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:R.375
EDO.8: 7 residues within 4Å:- Chain A: R.321, D.339, M.367, D.370, E.371, L.374
- Ligands: EDO.5
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:R.321, A:E.371
EDO.9: 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.10: 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.11: 4 residues within 4Å:- Chain A: G.233, Y.234, R.293, L.319
1 PLIP interactions:1 interactions with chain A- Water bridges: A:Y.234
EDO.12: 6 residues within 4Å:- Chain A: R.379, V.383, I.384, D.385, L.441
- Ligands: EDO.7
1 PLIP interactions:1 interactions with chain A- Water bridges: A:R.379
EDO.13: 1 residues within 4Å:- Chain A: H.273
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:H.273
EDO.14: 6 residues within 4Å:- Chain A: W.195, Y.197, E.210, A.308, N.310
- Ligands: S2G.18
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:G.190
- Water bridges: A:N.310
EDO.15: 9 residues within 4Å:- Chain A: Y.134, G.135, Y.197, V.198, G.199, S.203, S.204, N.300
- Ligands: S2G.18
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:V.198, A:S.204, A:N.300
- Water bridges: A:K.226
EDO.16: 7 residues within 4Å:- Chain A: E.340, C.343, K.344, S.347, E.392, F.409, Y.445
5 PLIP interactions:5 interactions with chain A- Hydrogen bonds: A:E.340, A:S.347, A:S.347, A:Y.445
- Water bridges: A:R.444
EDO.17: 1 residues within 4Å:- Chain A: H.27
No protein-ligand interaction detected (PLIP)- 1 x S2G: (2S)-2-HYDROXYPENTANEDIOIC ACID(Non-covalent)
- 1 x CL: CHLORIDE ION(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 L-2-Hydroxyglutarate. To be Published
- Release Date
- 2017-03-22
- Peptides
- LYSINE-SPECIFIC DEMETHYLASE 5B: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 2.05 Å
- Oligo State
- monomer
- Ligands
- 2 x ZN: ZINC ION(Non-covalent)
- 1 x MN: MANGANESE (II) ION(Non-covalent)
- 1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)
- 13 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 1 x S2G: (2S)-2-HYDROXYPENTANEDIOIC ACID(Non-covalent)
- 1 x CL: CHLORIDE ION(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 L-2-Hydroxyglutarate. To be Published
- Release Date
- 2017-03-22
- Peptides
- LYSINE-SPECIFIC DEMETHYLASE 5B: A
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
A