SMTL ID : 5a1f.1

Crystal structure of the catalytic domain of PLU1 in complex with N-oxalylglycine.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

monomer

Ligands

2 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 ZN.2: 4 residues within 4Å: Chain A: C.411, C.413, C.428, C.430 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.411, A:C.413, A:C.428, A:C.430

1 x OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.3: 13 residues within 4Å: Chain A: Y.193, F.201, H.204, E.206, S.212, N.214, K.222, W.224, H.292, A.304 Ligands: MN.5, EDO.12, EDO.13 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.212, A:N.214 Salt bridges: A:K.222, A:H.292

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

MN.4: 5 residues within 4Å: Chain A: L.67, N.68, L.118, T.121, E.124 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:L.67, A:L.118, A:T.121, A:E.124 MN.5: 4 residues within 4Å: Chain A: H.204, E.206, H.292 Ligands: OGA.3 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.204, A:E.206, A:H.292, H2O.4

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

PO4.6: 3 residues within 4Å: Chain A: H.327, K.399, H.423 3 PLIP interactions: 3 interactions with chain A Water bridges: A:H.423 Salt bridges: A:H.327, A:H.423

1 x EPE: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID(Non-functional Binders)

EPE.7: 14 residues within 4Å: Chain A: I.205, W.209, E.236, M.239, L.246, F.247, L.257, V.258, R.289, Y.291, H.322, Y.323, L.326, R.328 8 PLIP interactions: 8 interactions with chain A Water bridges: A:W.203, A:R.328, A:R.328, A:R.328 Salt bridges: A:E.236, A:R.289, A:H.322, A:R.328

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

EDO.8: 7 residues within 4Å: Chain A: I.180, A.182, F.332, S.333, E.336, M.337, R.395 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.333, A:R.395 EDO.9: 8 residues within 4Å: Chain A: D.393, E.394, R.395, Q.396, V.398, G.416, L.417, L.418 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.393, A:Q.396, A:L.418, A:L.418 EDO.10: 4 residues within 4Å: Chain A: R.375, V.379, I.380, L.437 No protein-ligand interaction detected (PLIP) EDO.11: 8 residues within 4Å: Chain A: A.91, D.92, K.95, M.196, C.197, E.220, G.298, F.299 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.92, A:C.197, A:E.220, A:F.299 EDO.12: 7 residues within 4Å: Chain A: Y.130, Y.193, S.199, S.200, K.222, N.296 Ligands: OGA.3 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.200, A:K.222, A:N.296 Water bridges: A:G.195 EDO.13: 6 residues within 4Å: Chain A: W.191, Y.193, E.206, A.304, N.306 Ligands: OGA.3 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.306 Water bridges: A:G.186, A:N.306 EDO.14: 5 residues within 4Å: Chain A: D.335, C.404, F.405, M.406, S.407 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:D.335, A:F.405, A:M.406, A:S.407, A:S.407 Water bridges: A:D.335

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Johansson, C. et al., Structural Analysis of Human Kdm5B Guides Histone Demethylase Inhibitor Development. Nat.Chem.Biol. (2016)

Release Date

2015-05-06

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