SMTL ID : 5fyv.1

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.87 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

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

MN.2: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: OAA.21 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.7, H2O.7

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.3: 13 residues within 4Å: Chain A: I.209, W.213, E.240, M.243, L.250, F.251, L.261, R.293, Y.295, H.326, Y.327, L.330, R.332 6 PLIP interactions: 6 interactions with chain A Water bridges: A:W.207 Salt bridges: A:E.240, A:R.293, A:H.326, A:R.332 pi-Cation interactions: A:F.251

17 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.6 Ligand excluded by PLIP EDO.5: 4 residues within 4Å: Chain A: R.375, L.441, Y.443, T.446 Ligand excluded by PLIP EDO.6: 7 residues within 4Å: Chain A: R.321, D.339, M.367, D.370, E.371, L.374 Ligands: EDO.4 Ligand excluded by PLIP EDO.7: 4 residues within 4Å: Chain A: P.7, P.276, V.277, Y.278 Ligand excluded by PLIP EDO.8: 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.9: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 Ligand excluded by PLIP EDO.10: 5 residues within 4Å: Chain A: R.379, V.383, I.384, D.385, L.441 Ligand excluded by PLIP EDO.11: 1 residues within 4Å: Chain A: H.273 Ligand excluded by PLIP EDO.12: 9 residues within 4Å: Chain A: Y.134, G.135, Y.197, V.198, G.199, S.203, S.204, N.300 Ligands: OAA.21 Ligand excluded by PLIP EDO.13: 8 residues within 4Å: Chain A: W.195, Y.197, E.210, S.216, A.308, V.309, N.310 Ligands: OAA.21 Ligand excluded by PLIP EDO.14: 4 residues within 4Å: Chain A: H.108, G.223, E.224, A.284 Ligand excluded by PLIP EDO.15: 2 residues within 4Å: Chain A: L.394, E.398 Ligand excluded by PLIP EDO.16: 6 residues within 4Å: Chain A: E.340, C.343, K.344, S.347, F.409, Y.445 Ligand excluded by PLIP EDO.17: 2 residues within 4Å: Chain A: E.387, K.440 Ligand excluded by PLIP EDO.18: 3 residues within 4Å: Chain A: F.205, C.206, H.208 Ligand excluded by PLIP EDO.19: 5 residues within 4Å: Chain A: M.94, F.98, T.131, V.132, E.133 Ligand excluded by PLIP EDO.20: 2 residues within 4Å: Chain A: S.414, L.422 Ligand excluded by PLIP

1 x OAA: OXALOACETATE ION(Non-covalent)

OAA.21: 10 residues within 4Å: Chain A: Y.197, F.205, H.208, N.218, K.226, W.228, H.296 Ligands: MN.2, EDO.12, EDO.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:F.205, A:W.228 Hydrogen bonds: A:N.218 Salt bridges: A:H.208, A:K.226, A:H.296

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

CL.22: 6 residues within 4Å: Chain A: L.67, N.68, L.122, V.123, T.125, E.128 Ligand excluded by PLIP

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

PO4.23: 3 residues within 4Å: Chain A: H.331, K.403, H.427 5 PLIP interactions: 5 interactions with chain A Water bridges: A:H.331, A:E.430 Salt bridges: A:H.331, A:K.403, 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 Oxaloacetate. To be Published

Release Date

2017-03-22

Peptides

LYSINE-SPECIFIC DEMETHYLASE 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 5B

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