SMTL ID : 5fy1.1 (1 other biounit)

Crystal structure of JmjC domain of human histone demethylase UTY in complex with N08619b

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.78 Å

Oligo State

monomer

Ligands

1 x ZN: ZINC ION(Non-covalent)

ZN.1: 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

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

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

2 x 0R0: 2-hydroxybenzonitrile(Non-covalent)

0R0.3: 2 residues within 4Å: Chain A: M.68, H.100 No protein-ligand interaction detected (PLIP) 0R0.4: 5 residues within 4Å: Chain A: T.416, E.418, T.436, N.442, F.443 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.442, A:N.442

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

DMS.5: 6 residues within 4Å: Chain A: Y.206, K.208, T.214, N.227, V.299, N.307 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.227 pi-Cation interactions: A:Y.206 DMS.6: 7 residues within 4Å: Chain A: N.220, N.221, L.260, R.326, N.330, K.336, P.338 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.330 Water bridges: A:R.326

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

EDO.7: 8 residues within 4Å: Chain A: S.56, T.57, Q.110, G.231, P.232, N.306 Ligands: EDO.8, EDO.12 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.57, A:N.306 Water bridges: A:T.57, A:T.57, A:K.58 EDO.8: 5 residues within 4Å: Chain A: Q.110, F.114, P.232, W.304 Ligands: EDO.7 No protein-ligand interaction detected (PLIP) EDO.9: 4 residues within 4Å: Chain A: N.8, P.9, P.10, R.280 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.8, A:R.280 Water bridges: A:T.11, A:R.280 EDO.10: 5 residues within 4Å: Chain A: H.391, E.397, H.400, L.413, Y.425 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.425 EDO.11: 7 residues within 4Å: Chain A: G.43, L.44, A.45, G.46, P.285, G.286, D.287 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:G.43, A:G.46 Water bridges: A:A.45 EDO.12: 7 residues within 4Å: Chain A: L.52, G.53, S.56, I.230, G.231, P.232 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.52, A:G.231 EDO.13: 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.14: 4 residues within 4Å: Chain A: P.232, G.233, G.303, W.304 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:W.304 Water bridges: A:D.234 EDO.15: 8 residues within 4Å: Chain A: P.34, P.37, E.242, N.292, A.293, T.295, C.318, L.322 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.242 EDO.16: 7 residues within 4Å: Chain A: G.199, Q.204, Y.206, E.219, A.309, W.310, N.311 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.204, A:Y.206, A:E.219 EDO.17: 5 residues within 4Å: Chain A: K.353, V.354, S.355, D.356, L.359 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.353, A:S.355, A:D.356 EDO.18: 4 residues within 4Å: Chain A: L.171, L.174, V.183, V.184 3 PLIP interactions: 3 interactions with chain A Water bridges: A:V.183, A:V.183, A:V.183 EDO.19: 6 residues within 4Å: Chain A: R.93, C.94, E.95, S.96, S.262, S.263 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.96, A:S.262, A:S.263 EDO.20: 3 residues within 4Å: Chain A: I.455, Y.458, D.459 No protein-ligand interaction detected (PLIP)

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 N08619B. 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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