SMTL ID : 5fym.1 (1 other biounit)

Crystal structure of JmjC domain of human histone demethylase UTY in complex with D-2-hydroxyglutarate

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.217, E.219, H.297 Ligands: 2HG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.217, A:E.219, A:H.297, H2O.6

1 x 2HG: (2R)-2-hydroxypentanedioic acid(Non-covalent)

2HG.2: 14 residues within 4Å: Chain A: F.155, K.208, T.214, H.217, E.219, S.225, N.227, W.237, H.297, V.299, N.307, A.309 Ligands: MN.1, EDO.13 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:T.214 Hydrogen bonds: A:S.225, A:N.227 Water bridges: A:T.214 Salt bridges: A:K.208, A:H.297

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

EDO.3: 8 residues within 4Å: Chain A: S.56, T.57, Q.110, G.231, P.232, N.306 Ligands: EDO.4, EDO.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:T.57, A:N.306 Water bridges: A:K.58 EDO.4: 7 residues within 4Å: Chain A: Q.110, A.111, F.114, P.232, W.304 Ligands: EDO.3, EDO.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.110 EDO.5: 2 residues within 4Å: Chain A: N.8, R.280 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:R.280 Water bridges: A:R.280, A:R.280 EDO.6: 5 residues within 4Å: Chain A: H.391, H.400, L.413, Y.425, V.427 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:H.391, A:Y.425 EDO.7: 7 residues within 4Å: Chain A: G.43, L.44, A.45, G.46, P.285, G.286, D.287 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:G.43, A:A.45, A:G.46 Water bridges: A:A.45, A:P.285, A:D.287, A:D.287, A:D.287 EDO.8: 7 residues within 4Å: Chain A: L.52, G.53, S.56, I.230, G.231, P.232 Ligands: EDO.3 1 PLIP interactions: 1 interactions with chain A Water bridges: A:S.56 EDO.9: 7 residues within 4Å: Chain A: T.32, C.224, N.292, P.314, T.316, C.318, Q.319 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.316 EDO.10: 5 residues within 4Å: Chain A: P.232, G.233, G.303, W.304 Ligands: EDO.4 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.304, A:W.304 Water bridges: A:D.234 EDO.11: 7 residues within 4Å: Chain A: P.34, E.242, N.292, A.293, T.295, C.318, L.322 4 PLIP interactions: 4 interactions with chain A Water bridges: A:E.242, A:E.242, A:D.243, A:D.243 EDO.12: 4 residues within 4Å: Chain A: Q.373, L.377, H.430, D.431 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.373, A:H.430, A:D.431 EDO.13: 8 residues within 4Å: Chain A: G.199, Q.204, Y.206, E.219, A.309, W.310, N.311 Ligands: 2HG.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.199, A:Q.204, A:Y.206 EDO.14: 5 residues within 4Å: Chain A: H.28, A.179, F.180, S.185, G.187 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:H.28, A:S.185, A:G.187 Water bridges: A:F.180 EDO.15: 5 residues within 4Å: Chain A: K.6, L.7, Y.244, N.275, P.277 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.275 EDO.16: 3 residues within 4Å: Chain A: I.14, P.26, L.27 No protein-ligand interaction detected (PLIP)

1 x ZN: ZINC ION(Non-covalent)

ZN.17: 4 residues within 4Å: Chain A: C.402, C.405, C.429, C.432 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.402, A:C.405, A:C.429, A:C.432

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Nowak, R. et al., Crystal Structure of Jmjc Domain of Human Histone Demethylase Uty in Complex with D-2- Hydroxyglutarate. To be Published

Release Date

2016-03-16

Peptides

HISTONE DEMETHYLASE UTY: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HISTONE DEMETHYLASE UTY

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