SMTL ID : 6ej1.1

Crystal structure of KDM5B in complex with KDOPZ48a.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.07 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.397, C.400, C.420, H.423 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.397, A:C.400, A:C.420, A:H.423

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

MN.2: 5 residues within 4Å: Chain A: L.66, N.67, L.118, T.121, E.124 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:T.121 MN.3: 4 residues within 4Å: Chain A: H.204, E.206, H.292 Ligands: B7Q.7 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.204, A:E.206, A:H.292, H2O.2, H2O.4

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

DMS.4: 7 residues within 4Å: Chain A: W.191, Y.193, E.206, S.212, A.304, V.305, N.306 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:E.206 DMS.5: 5 residues within 4Å: Chain A: I.205, W.209, H.322, Y.323, R.328 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.328 DMS.6: 7 residues within 4Å: Chain A: E.336, C.339, K.340, E.388, F.405, R.440, Y.441 2 PLIP interactions: 2 interactions with chain A Water bridges: A:E.336 Salt bridges: A:E.388

1 x B7Q: 5-[1-[1-(2-chloranylethanoyl)piperidin-4-yl]pyrazol-4-yl]-7-oxidanylidene-6-propan-2-yl-4~{H}-pyrazolo[1,5-a]pyrimidine-3-carbonitrile(Non-covalent)

B7Q.7: 16 residues within 4Å: Chain A: R.62, R.74, Y.130, G.131, W.191, Y.193, S.200, F.201, H.204, N.214, K.222, W.224, H.292, N.296 Ligands: MN.3, EDO.8 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.130, A:W.191, A:Y.193, A:Y.193 Hydrogen bonds: A:Y.193, A:N.214, A:N.296 Water bridges: A:K.222 pi-Stacking: A:Y.193, A:Y.193, A:F.201

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

EDO.8: 8 residues within 4Å: Chain A: Q.64, Q.72, Y.130, S.200, F.201, C.202, H.204 Ligands: B7Q.7 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.64, A:Q.72, A:C.202, A:H.204 EDO.9: 7 residues within 4Å: Chain A: F.59, G.131, A.132, D.133, F.139, L.192, V.194 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.131, A:V.194

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

srikannathasan, v., Crystal structure of KDM5B in complex with KDOPZ48a. 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