SMTL ID : 5fzf.1

Crystal structure of the catalytic domain of human JARID1B in complex with MC3962

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.97 Å

Oligo State

monomer

Ligands

2 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 ZN.2: 4 residues within 4Å: Chain A: C.415, C.417, C.432, C.434 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.415, A:C.417, A:C.432, A:C.434

2 x UUN: N-hydroxy-2-[(6-oxo-4-phenyl-1,6-dihydropyrimidin-2-yl)sulfanyl]acetamide(Non-covalent)

UUN.3: 7 residues within 4Å: Chain A: E.8, C.9, P.10, V.11, I.32, T.36, Y.278 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:P.10, A:I.32, A:T.36, A:Y.278 Hydrogen bonds: A:V.11 UUN.27: 16 residues within 4Å: Chain A: R.75, Y.134, Y.197, F.205, H.208, E.210, S.216, N.218, K.226, W.228, H.296, N.300 Ligands: MN.4, DMS.23, DMS.24, DMS.26 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.134, A:Y.197 Hydrogen bonds: A:S.216, A:N.218, A:N.218, A:K.226, A:N.300 Water bridges: A:R.75, A:R.75, A:G.199 pi-Stacking: A:Y.197

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

MN.4: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: UUN.27 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.3, UUN.27

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

CL.5: 5 residues within 4Å: Chain A: L.67, N.68, L.122, T.125, E.128 Ligand excluded by PLIP

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

EDO.6: 5 residues within 4Å: Chain A: D.339, C.408, F.409, M.410, S.411 Ligand excluded by PLIP EDO.7: 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.8: 5 residues within 4Å: Chain A: R.375, S.386, L.441, Y.443, T.446 Ligand excluded by PLIP EDO.9: 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.10: 4 residues within 4Å: Chain A: P.7, M.271, P.276, V.277 Ligand excluded by PLIP EDO.11: 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.12: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 Ligand excluded by PLIP EDO.13: 5 residues within 4Å: Chain A: R.379, V.383, I.384, D.385, L.441 Ligand excluded by PLIP EDO.14: 2 residues within 4Å: Chain A: H.273, E.274 Ligand excluded by PLIP EDO.15: 4 residues within 4Å: Chain A: M.2, K.117, E.118, R.121 Ligand excluded by PLIP EDO.16: 5 residues within 4Å: Chain A: V.324, E.325, R.328, T.406 Ligands: EDO.9 Ligand excluded by PLIP EDO.17: 6 residues within 4Å: Chain A: I.209, W.213, H.326, Y.327, L.330, R.332 Ligand excluded by PLIP EDO.18: 4 residues within 4Å: Chain A: W.16, W.47, Y.163, S.166 Ligand excluded by PLIP EDO.19: 8 residues within 4Å: Chain A: F.51, A.52, C.53, L.58, G.144, S.145, G.146, F.305 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: L.394, E.398 Ligand excluded by PLIP EDO.21: 4 residues within 4Å: Chain A: E.387, R.388, M.389, R.442 Ligand excluded by PLIP EDO.22: 5 residues within 4Å: Chain A: T.377, L.425, H.426, H.427, V.428 Ligand excluded by PLIP

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

DMS.23: 9 residues within 4Å: Chain A: Q.65, Q.73, T.74, Y.134, S.204, F.205, C.206, V.262 Ligands: UUN.27 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:C.206 Water bridges: A:R.75 DMS.24: 9 residues within 4Å: Chain A: W.195, Y.197, E.210, S.216, A.308, V.309, N.310 Ligands: DMS.26, UUN.27 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.75 Salt bridges: A:E.210 DMS.25: 7 residues within 4Å: Chain A: E.340, K.344, S.347, E.392, F.409, R.444, Y.445 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.340 Salt bridges: A:E.392 DMS.26: 6 residues within 4Å: Chain A: R.75, V.76, W.195, Y.197 Ligands: DMS.24, UUN.27 1 PLIP interactions: 1 interactions with chain A pi-Cation interactions: A:W.195

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

PO4.28: 3 residues within 4Å: Chain A: E.387, K.440, R.442 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:E.387 Salt bridges: A:K.440, A:R.442 PO4.29: 3 residues within 4Å: Chain A: H.331, K.403, H.427 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:H.331, A:H.427

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 Mc3962. 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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