SMTL ID : 5fup.1

Crystal structure of human JARID1B in complex with 2-oxoglutarate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.15 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: 5 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: AKG.7, EDO.16 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.10 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: 12 residues within 4Å: Chain A: I.209, W.213, E.240, L.250, F.251, L.261, V.262, Y.295, H.326, Y.327, L.330, R.332 7 PLIP interactions: 7 interactions with chain A Water bridges: A:L.261, A:L.261, A:R.332 Salt bridges: A:E.240, A:H.326, A:R.332 pi-Cation interactions: A:F.251

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

CL.6: 5 residues within 4Å: Chain A: L.67, N.68, L.122, T.125, E.128 Ligand excluded by PLIP

1 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.7: 13 residues within 4Å: Chain A: Y.134, Y.197, F.205, H.208, E.210, S.216, N.218, K.226, W.228, H.296, A.308 Ligands: MN.3, EDO.16 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.197, A:F.205, A:W.228 Hydrogen bonds: A:Y.134, A:S.216, A:N.218 Salt bridges: A:K.226, A:H.296

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

EDO.8: 6 residues within 4Å: Chain A: D.339, C.408, F.409, M.410, S.411 Ligands: EDO.10 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.9: 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.10: 6 residues within 4Å: Chain A: R.321, D.339, M.367, D.370, E.371 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.321, A:D.339, A:M.367 EDO.11: 5 residues within 4Å: Chain A: P.7, M.271, P.276, V.277, Y.278 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.278 EDO.12: 8 residues within 4Å: Chain A: D.397, E.398, R.399, Q.400, V.402, G.420, L.421, L.422 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.397, A:Q.400, A:V.402, A:L.422, A:L.422 EDO.13: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.293 EDO.14: 5 residues within 4Å: Chain A: R.379, V.383, I.384, D.385, L.441 No protein-ligand interaction detected (PLIP) EDO.15: 4 residues within 4Å: Chain A: W.16, W.47, E.162, S.166 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.162 EDO.16: 7 residues within 4Å: Chain A: W.195, Y.197, E.210, A.308, N.310 Ligands: MN.3, AKG.7 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.197, A:N.310, A:N.310 Water bridges: A:R.75, A:Y.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, C. et al., Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development. Nat.Chem.Biol. (2016)

Release Date

2016-03-23

Peptides

LYSINE-SPECIFIC DEMETHYLASE 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 5B

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