SMTL ID : 6rbi.1

Crystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.21 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.9: 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 MN: MANGANESE (II) ION(Non-covalent)

MN.2: 4 residues within 4Å: Chain A: H.208, E.210, H.296 Ligands: JX8.5 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.208, A:E.210, H2O.4, H2O.4, JX8.5

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

PO4.3: 3 residues within 4Å: Chain A: H.331, K.403, H.427 4 PLIP interactions: 4 interactions with chain A Water bridges: A:R.328, A:H.427 Salt bridges: A:H.331, A:H.427

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

EDO.4: 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.6: 3 residues within 4Å: Chain A: G.233, Y.234, R.293 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.293 Water bridges: A:G.233, A:P.292 EDO.7: 7 residues within 4Å: Chain A: Q.65, Q.73, Y.134, S.204, F.205, C.206, H.208 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.65, A:Q.73, A:C.206, A:H.208 EDO.8: 7 residues within 4Å: Chain A: E.340, C.343, K.344, E.392, F.409, R.444, Y.445 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.340, A:E.392, A:R.444, A:Y.445

1 x JX8: 5-(1~{H}-1,2,3,4-tetrazol-5-yl)quinolin-8-ol(Non-covalent)

JX8.5: 10 residues within 4Å: Chain A: Y.197, F.205, H.208, E.210, N.218, K.226, W.228, H.296, N.300 Ligands: MN.2 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:Y.197, A:Y.197, A:F.205, A:W.228 Hydrogen bonds: A:N.300 Water bridges: A:S.204, A:S.216, A:K.226 pi-Stacking: A:Y.197, A:F.205

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

NA.10: 5 residues within 4Å: Chain A: L.67, N.68, L.122, T.125, E.128 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.122 NA.11: 4 residues within 4Å: Chain A: I.209, W.213, H.326, Y.327 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:W.213

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, C. et al., Crystal structure of KDM5B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol. To Be Published

Release Date

2020-05-13

Peptides

Lysine-specific demethylase 5B,Lysine-specific demethylase 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 5B,Lysine-specific demethylase 5B

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