SMTL ID : 5a3p.1

Crystal structure of the catalytic domain of human PLU1 (JARID1B).

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.01 Å

Oligo State

monomer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.401, C.404, C.424, H.427 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.401, A:C.404, A:C.424, A:H.427 ZN.2: 4 residues within 4Å: Chain A: C.415, C.417, C.432, C.434 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.415, A:C.417, A:C.432, A:C.434

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

MN.3: 6 residues within 4Å: Chain A: L.67, N.68, L.122, V.123, T.125, E.128 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:L.122, A:T.125, A:E.128, H2O.5 MN.4: 3 residues within 4Å: Chain A: H.208, E.210, H.296 6 PLIP interactions: 3 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:H.208, A:E.210, A:H.296, H2O.11, H2O.11, H2O.12 MN.5: 2 residues within 4Å: Chain A: H.331, H.427 No protein-ligand interaction detected (PLIP)

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

EPE.6: 12 residues within 4Å: Chain A: I.209, W.213, E.240, M.243, L.250, F.251, L.261, Y.295, H.326, Y.327, L.330, R.332 7 PLIP interactions: 7 interactions with chain A Water bridges: A:W.207, A:R.293, A:R.332 Salt bridges: A:E.240, A:H.326, A:R.332 pi-Cation interactions: A:F.251

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

EDO.7: 6 residues within 4Å: Chain A: W.195, Y.197, E.210, A.308, V.309, N.310 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.195 Water bridges: A:Y.197, A:N.310 EDO.8: 6 residues within 4Å: Chain A: D.339, C.408, F.409, M.410, S.411 Ligands: EDO.11 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:D.339, A:F.409, A:M.410, A:S.411, A:S.411 EDO.9: 8 residues within 4Å: Chain A: F.60, G.135, A.136, D.137, F.143, L.196, Y.197, V.198 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.135, A:D.137, A:V.198 Water bridges: A:D.137 EDO.10: 4 residues within 4Å: Chain A: R.375, L.441, Y.443, T.446 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.375 EDO.11: 7 residues within 4Å: Chain A: R.321, D.339, M.367, D.370, E.371, L.374 Ligands: EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.321, A:D.339, A:M.367 EDO.12: 5 residues within 4Å: Chain A: P.7, M.271, P.276, V.277, Y.278 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.278 EDO.13: 8 residues within 4Å: Chain A: D.397, E.398, R.399, Q.400, V.402, G.420, L.421, L.422 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.397, A:Q.400, A:L.422, A:L.422 EDO.14: 4 residues within 4Å: Chain A: G.233, Y.234, R.293, L.319 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.293 EDO.15: 4 residues within 4Å: Chain A: R.379, V.383, I.384, L.441 1 PLIP interactions: 1 interactions with chain A Water bridges: A:R.379 EDO.16: 5 residues within 4Å: Chain A: Y.134, Y.197, S.203, S.204, N.300 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.203, A:N.300 EDO.17: 6 residues within 4Å: Chain A: W.16, F.19, A.20, W.47, S.166, W.168 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:F.19 Water bridges: A:G.167

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

2015-06-10

Peptides

LYSINE-SPECIFIC DEMETHYLASE 5B: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

LYSINE-SPECIFIC DEMETHYLASE 5B

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