SMTL ID : 6rbj.1 (1 other biounit)

Crystal structure of KDM3B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

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

EDO.1: 11 residues within 4Å: Chain A: R.175, T.212, E.215, G.216, L.236, H.238, Y.276, D.278, Q.279, R.282, H.315 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.215, A:Y.276, A:R.282, A:R.282 EDO.2: 8 residues within 4Å: Chain A: K.107, L.108, K.109, D.110, K.162, M.163, Y.164 Ligands: JX8.3 3 PLIP interactions: 3 interactions with chain A Water bridges: A:L.108, A:D.110, A:Y.164

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

JX8.3: 13 residues within 4Å: Chain A: Y.164, T.179, T.180, H.183, D.185, N.191, W.237, I.306, H.312, V.314, K.322 Ligands: EDO.2, MN.4 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.164, A:T.180, A:W.237, A:V.314 Hydrogen bonds: A:T.180, A:T.180, A:N.191, A:H.312, A:K.322 Water bridges: A:N.316, A:N.316 pi-Stacking: A:Y.164

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

MN.4: 4 residues within 4Å: Chain A: H.183, D.185, H.312 Ligands: JX8.3 5 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.183, A:D.185, H2O.2, H2O.2, JX8.3

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

CL.5: 5 residues within 4Å: Chain A: W.25, L.134, P.135, E.136, Y.137 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, C. et al., Crystal structure of KDM3B in complex with 5-(1H-tetrazol-5-yl)quinolin-8-ol. To Be Published

Release Date

2020-05-13

Peptides

Lysine-specific demethylase 3B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 3B

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