SMTL ID : 5fpu.1

Crystal structure of human JARID1B in complex with GSKJ1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.24 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 2 PLIP interactions: 2 interactions with chain A Metal complexes: A:C.415, A:C.432

1 x K0I: 3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoic acid(Non-covalent)

K0I.3: 16 residues within 4Å: Chain A: Q.65, Q.73, T.74, R.75, K.77, Y.134, Y.197, S.204, F.205, H.208, E.210, D.211, N.218, K.226, A.306 Ligands: MN.5 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:Y.134, A:Y.197, A:Y.197, A:F.205 Hydrogen bonds: A:Y.197, A:N.218 Water bridges: A:H.296 Salt bridges: A:K.226

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

MN.4: 5 residues within 4Å: Chain A: L.67, N.68, L.122, T.125, E.128 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.122, A:T.125, A:E.128, H2O.2 MN.5: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: K0I.3 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, H2O.5, H2O.5

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

PO4.6: 3 residues within 4Å: Chain A: H.331, K.403, H.427 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.427 Salt bridges: A:H.331, A:H.427 PO4.7: 6 residues within 4Å: Chain A: W.195, Y.197, E.210, A.308, V.309, N.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.195 Water bridges: A:S.216, A:N.310

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

EPE.8: 11 residues within 4Å: Chain A: I.209, W.213, E.240, F.251, Q.260, R.293, Y.295, H.326, Y.327, L.330, R.332 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.327 Salt bridges: A:E.240, A:E.240, A:R.293, A:R.332

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

EDO.9: 7 residues within 4Å: Chain A: I.184, A.186, F.336, S.337, E.340, M.341, R.399 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.337, A:R.399 EDO.10: 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.11: 4 residues within 4Å: Chain A: R.379, V.383, I.384, L.441 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.379, A:R.379 EDO.12: 9 residues within 4Å: Chain A: A.95, D.96, K.99, V.107, M.200, C.201, E.224, G.302, F.303 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.96, A:C.201, A:F.303 Water bridges: A:E.224 EDO.13: 5 residues within 4Å: Chain A: D.339, C.408, F.409, M.410, S.411 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.339, A:F.409, A:M.410, A:S.411, A:S.411

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

2016-01-13

Peptides

LYSINE-SPECIFIC DEMETHYLASE 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 5B

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