SMTL ID : 6rbj.2 (1 other biounit)

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

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.09 Å

Oligo State

monomer

Ligands

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

EDO.1: 10 residues within 4Å: Chain A: R.156, L.159, G.160, P.161, K.162, Y.164, A.189, A.324, E.325, D.326 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.156, A:E.325, A:E.325, A:D.326 EDO.2: 4 residues within 4Å: Chain A: D.65, V.66, D.67, D.79 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.79, A:D.79 EDO.3: 7 residues within 4Å: Chain A: N.70, N.73, A.75, I.77, S.98, E.99, M.104 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.70, A:N.73, A:N.73, A:E.99

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

JX8.4: 12 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: MN.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.164, A:Y.164, 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.5: 4 residues within 4Å: Chain A: H.183, D.185, H.312 Ligands: JX8.4 5 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions, 1 Ligand-Ligand interactions Metal complexes: A:H.183, A:D.185, A:D.185, H2O.1, JX8.4

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
B

Lysine-specific demethylase 3B

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