SMTL ID : 5fys.1

Crystal structure of the catalytic domain of human JARID1B in complex with D-2-hydroxyglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.89 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 MN: MANGANESE (II) ION(Non-covalent)

MN.3: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: 2HG.20 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.4 MN.4: 2 residues within 4Å: Chain A: H.331, H.427 No protein-ligand interaction detected (PLIP)

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

EPE.5: 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 Water bridges: A:W.207, A:R.332 Salt bridges: A:E.240, A:R.293, A:H.326, A:R.332 pi-Cation interactions: A:F.251

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

EDO.6: 6 residues within 4Å: Chain A: D.339, C.408, F.409, M.410, S.411 Ligands: EDO.9 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.7: 8 residues within 4Å: Chain A: F.60, G.135, A.136, D.137, F.143, L.196, Y.197, V.198 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.135, A:D.137, A:D.137, A:V.198 EDO.8: 5 residues within 4Å: Chain A: R.375, S.386, L.441, Y.443, T.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.375 EDO.9: 7 residues within 4Å: Chain A: R.321, D.339, M.367, D.370, E.371, L.374 Ligands: EDO.6 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:R.321, A:D.339, A:M.367 Water bridges: A:D.339, A:D.370 EDO.10: 4 residues within 4Å: Chain A: P.7, P.276, V.277, Y.278 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.278 EDO.11: 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.12: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 No protein-ligand interaction detected (PLIP) EDO.13: 4 residues within 4Å: Chain A: R.379, V.383, I.384, L.441 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.379 EDO.14: 7 residues within 4Å: Chain A: Y.134, Y.197, S.203, S.204, F.205, N.300 Ligands: 2HG.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.203, A:N.300 EDO.15: 1 residues within 4Å: Chain A: H.273 No protein-ligand interaction detected (PLIP) EDO.16: 6 residues within 4Å: Chain A: W.195, Y.197, E.210, A.308, N.310 Ligands: 2HG.20 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.195 Water bridges: A:N.310 EDO.17: 1 residues within 4Å: Chain A: D.85 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.85 EDO.18: 5 residues within 4Å: Chain A: E.13, R.42, P.43, P.44, P.45 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:P.43 EDO.19: 1 residues within 4Å: Chain A: H.27 No protein-ligand interaction detected (PLIP)

1 x 2HG: (2R)-2-hydroxypentanedioic acid(Non-covalent)

2HG.20: 12 residues within 4Å: Chain A: Y.197, F.205, H.208, E.210, S.216, N.218, W.228, H.296, A.308 Ligands: MN.3, EDO.14, EDO.16 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.197, A:Y.197, A:F.205 Hydrogen bonds: A:E.210, A:S.216, A:N.218, A:H.296 Water bridges: A:H.208 Salt bridges: A:H.208, A:H.296

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

CL.21: 6 residues within 4Å: Chain A: L.67, N.68, L.122, V.123, T.125, 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 D-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

LYSINE-SPECIFIC DEMETHYLASE 5B

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