SMTL ID : 5a3w.1

Crystal structure of human PLU-1 (JARID1B) in complex with Pyridine-2, 6-dicarboxylic Acid (PDCA)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 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

1 x NA: SODIUM ION(Non-functional Binders)

NA.3: 6 residues within 4Å: Chain A: L.67, N.68, L.122, V.123, T.125, E.128 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:V.123, A:T.125

1 x PD2: PYRIDINE-2,4-DICARBOXYLIC ACID(Non-covalent)

PD2.4: 11 residues within 4Å: Chain A: R.75, Y.134, Y.197, F.205, H.208, E.210, N.218, K.226, W.228, H.296 Ligands: MN.5 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.197, A:W.228 Hydrogen bonds: A:Y.134, A:Y.197 Water bridges: A:R.75, A:R.75, A:N.218 Salt bridges: A:R.75, A:H.208, A:K.226 pi-Stacking: A:F.205

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

MN.5: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: PD2.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.5

1 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

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

EPE.7: 13 residues within 4Å: Chain A: I.209, W.213, E.240, M.243, L.250, F.251, L.261, V.262, Y.295, H.326, Y.327, L.330, R.332 12 PLIP interactions: 12 interactions with chain A Hydrogen bonds: A:Y.327 Water bridges: A:W.207, A:E.210, A:W.213, A:H.326, A:R.332, A:R.332, A:R.332 Salt bridges: A:E.240, A:H.326, A:R.332 pi-Cation interactions: A:F.251

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

EDO.8: 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.9: 5 residues within 4Å: Chain A: R.379, V.383, I.384, S.386, L.441 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:I.384 Water bridges: A:R.379 EDO.10: 8 residues within 4Å: Chain A: A.95, D.96, K.99, 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:E.224, A:F.303

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

2015-06-17

Peptides

LYSINE-SPECIFIC DEMETHYLASE 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 5B

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