SMTL ID : 5fzi.1

Crystal structure of the catalytic domain of human JARID1B in complex with MC3095

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.95 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.401, C.404, C.424, H.427 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.401, A:C.404, A:C.424, A:H.427

2 x MN: MANGANESE (II) ION(Non-covalent)

MN.2: 3 residues within 4Å: Chain A: H.208, E.210, H.296 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.6, H2O.6, H2O.6 MN.3: 2 residues within 4Å: Chain A: H.331, H.427 No protein-ligand interaction detected (PLIP)

18 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.4: 6 residues within 4Å: Chain A: D.339, C.408, F.409, M.410, S.411 Ligands: EDO.16 Ligand excluded by PLIP EDO.5: 7 residues within 4Å: Chain A: F.60, G.135, A.136, D.137, F.143, L.196, V.198 Ligand excluded by PLIP EDO.6: 6 residues within 4Å: Chain A: R.375, S.386, L.441, Y.443, T.446 Ligands: EDO.11 Ligand excluded by PLIP EDO.7: 7 residues within 4Å: Chain A: R.321, D.339, M.367, D.370, E.371, L.374 Ligands: EDO.16 Ligand excluded by PLIP EDO.8: 4 residues within 4Å: Chain A: P.7, P.276, V.277, Y.278 Ligand excluded by PLIP EDO.9: 8 residues within 4Å: Chain A: D.397, E.398, R.399, Q.400, V.402, G.420, L.421, L.422 Ligand excluded by PLIP EDO.10: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 Ligand excluded by PLIP EDO.11: 5 residues within 4Å: Chain A: R.379, V.383, I.384, L.441 Ligands: EDO.6 Ligand excluded by PLIP EDO.12: 2 residues within 4Å: Chain A: H.273, E.274 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: W.16, D.46, W.47, E.162, Y.163 Ligand excluded by PLIP EDO.14: 3 residues within 4Å: Chain A: T.377, L.425, H.426 Ligand excluded by PLIP EDO.15: 5 residues within 4Å: Chain A: A.52, G.144, S.145, G.146, F.305 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: V.324, E.325, R.328, T.406 Ligands: EDO.4, EDO.7 Ligand excluded by PLIP EDO.17: 5 residues within 4Å: Chain A: M.94, F.98, T.131, V.132, E.133 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: K.429, L.431, C.432, S.433 Ligand excluded by PLIP EDO.19: 3 residues within 4Å: Chain A: S.416, C.417, K.438 Ligand excluded by PLIP EDO.20: 4 residues within 4Å: Chain A: F.51, H.221, W.222, A.284 Ligand excluded by PLIP EDO.21: 5 residues within 4Å: Chain A: M.243, L.250, F.251, L.261, Y.295 Ligand excluded by PLIP

3 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.22: 9 residues within 4Å: Chain A: Q.65, Q.73, T.74, V.76, Y.134, S.204, F.205, C.206 Ligands: FIG.25 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.206 DMS.23: 6 residues within 4Å: Chain A: W.195, Y.197, S.216, A.308, V.309, N.310 2 PLIP interactions: 2 interactions with chain A Water bridges: A:N.310 Salt bridges: A:E.210 DMS.24: 5 residues within 4Å: Chain A: I.209, W.213, H.326, Y.327, L.330 No protein-ligand interaction detected (PLIP)

1 x FIG: 6-oxo-2-[(2-oxo-2-phenylethyl)sulfanyl]-1,6-dihydropyrimidine-5-carboxylic acid(Non-covalent)

FIG.25: 10 residues within 4Å: Chain A: R.75, V.76, Y.197, F.205, H.208, I.209, N.218, K.226, Q.260 Ligands: DMS.22 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:R.75, A:F.205, A:H.208 Hydrogen bonds: A:V.76, A:N.218 Water bridges: A:N.300, A:N.300 Salt bridges: A:K.226 pi-Stacking: A:Y.197, A:H.208

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.26: 5 residues within 4Å: Chain A: C.343, K.344, E.392, F.409, Y.445 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.444, A:Y.445 Water bridges: A:E.340 Salt bridges: A:K.344

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.27: 6 residues within 4Å: Chain A: L.67, N.68, L.122, T.125, I.126, E.128 Ligand excluded by PLIP

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 Mc3095. To be Published

Release Date

2017-03-29

Peptides

LYSINE-SPECIFIC DEMETHYLASE 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 5B

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