SMTL ID : 6eiu.1

Crystal structure of KDM5B in complex with KDOPZ29a

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.88 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.400, C.403, C.423, H.426 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.400, A:C.403, A:C.423, A:H.426 ZN.17: 4 residues within 4Å: Chain A: C.414, C.416, C.431, C.433 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.414, A:C.431, A:C.433

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

MN.2: 5 residues within 4Å: Chain A: L.66, N.67, L.121, T.124, E.127 3 PLIP interactions: 2 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.66, A:E.127, H2O.1 MN.3: 4 residues within 4Å: Chain A: H.207, E.209, H.295 Ligands: B6T.4 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.207, A:E.209, A:H.295, H2O.2, H2O.6

1 x B6T: 8-oxidanyl-6-phenyl-7-propan-2-yl-imidazo[1,2-b]pyridazine-3-carbonitrile(Non-covalent)

B6T.4: 15 residues within 4Å: Chain A: R.74, Y.133, G.134, A.135, Y.196, S.203, F.204, H.207, N.217, K.225, W.227, H.295, N.299 Ligands: MN.3, DMS.5 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:Y.133, A:A.135, A:Y.196, A:Y.196, A:F.204 Hydrogen bonds: A:N.217, A:N.299 Water bridges: A:R.74, A:R.74, A:K.225 pi-Stacking: A:Y.196, A:F.204

7 x DMS: DIMETHYL SULFOXIDE(Non-functional Binders)

DMS.5: 8 residues within 4Å: Chain A: Q.64, Q.72, T.73, Y.133, S.203, F.204, C.205 Ligands: B6T.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.205 DMS.6: 5 residues within 4Å: Chain A: R.74, V.75, W.194, Y.196 Ligands: DMS.7 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.196 Water bridges: A:R.74 pi-Cation interactions: A:W.194 DMS.7: 8 residues within 4Å: Chain A: W.194, Y.196, E.209, S.215, A.307, V.308, N.309 Ligands: DMS.6 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.74 Salt bridges: A:E.209 DMS.8: 8 residues within 4Å: Chain A: I.208, W.212, E.239, R.292, H.325, Y.326, L.329, R.331 No protein-ligand interaction detected (PLIP) DMS.9: 2 residues within 4Å: Chain A: H.330, H.426 No protein-ligand interaction detected (PLIP) DMS.10: 7 residues within 4Å: Chain A: E.339, C.342, K.343, S.346, E.391, F.408, Y.444 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.339 Salt bridges: A:E.391 DMS.11: 6 residues within 4Å: Chain A: R.374, S.385, L.440, Y.442, T.445 Ligands: EDO.14 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.374 pi-Cation interactions: A:Y.442

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

EDO.12: 7 residues within 4Å: Chain A: F.59, G.134, A.135, D.136, F.142, L.195, V.197 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.134, A:V.197 EDO.13: 8 residues within 4Å: Chain A: V.323, Y.326, R.327, R.331, C.333, C.403, K.404, T.405 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:C.403 EDO.14: 5 residues within 4Å: Chain A: R.378, V.382, I.383, L.440 Ligands: DMS.11 1 PLIP interactions: 1 interactions with chain A Water bridges: A:I.383 EDO.15: 6 residues within 4Å: Chain A: R.320, D.338, M.366, D.369, E.370, L.373 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.320, A:D.338, A:M.366 EDO.16: 8 residues within 4Å: Chain A: D.396, E.397, R.398, Q.399, V.401, G.419, L.420, L.421 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.396, A:Q.399, A:L.421, A:L.421

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Srikannathasan, V., Crystal structure of KDM5B in complex with KDOPZ29a. to be published

Release Date

2018-05-02

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