SMTL ID : 3zpo.1 (1 other biounit)

Crystal structure of JmjC domain of human histone demethylase UTY with bound GSK J1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x K0I: 3-[[2-pyridin-2-yl-6-(1,2,4,5-tetrahydro-3-benzazepin-3-yl)pyrimidin-4-yl]amino]propanoic acid(Non-covalent)

K0I.1: 20 residues within 4Å: Chain A: R.72, Q.74, S.96, F.155, T.157, N.158, Y.206, K.208, R.213, T.214, P.215, H.217, E.219, N.220, N.227, S.263, V.299, N.307 Ligands: FE2.3, EDO.12 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:R.72, A:F.155, A:Y.206, A:T.214, A:P.215 Hydrogen bonds: A:T.214, A:T.214, A:N.227 Water bridges: A:Y.206, A:Y.206, A:T.214 Salt bridges: A:K.208

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 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 FE2: FE (II) ION(Non-covalent)

FE2.3: 4 residues within 4Å: Chain A: H.217, E.219, H.297 Ligands: K0I.1 4 PLIP interactions: 2 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:H.217, A:E.219, H2O.6, H2O.7

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

EDO.4: 4 residues within 4Å: Chain A: R.42, G.43, R.284, D.287 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:R.42, A:R.42, A:R.284 Water bridges: A:P.285, A:P.285, A:D.287 EDO.5: 7 residues within 4Å: Chain A: T.32, C.224, N.292, P.314, T.316, C.318, Q.319 No protein-ligand interaction detected (PLIP) EDO.6: 7 residues within 4Å: Chain A: P.34, N.36, P.37, N.292, A.293, C.318, L.322 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.36, A:N.292 Water bridges: A:E.242 EDO.7: 5 residues within 4Å: Chain A: N.64, N.65, E.66, H.67, K.166 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.66 Water bridges: A:N.65 EDO.8: 7 residues within 4Å: Chain A: S.56, T.57, Q.110, G.231, P.232, N.306 Ligands: EDO.9 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:T.57, A:T.57, A:N.306 Water bridges: A:K.58, A:Q.110, A:G.231 EDO.9: 5 residues within 4Å: Chain A: Q.110, A.111, F.114, W.304 Ligands: EDO.8 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.110 EDO.10: 4 residues within 4Å: Chain A: K.321, M.362, Y.365, C.366 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:M.362 EDO.11: 5 residues within 4Å: Chain A: I.91, W.92, R.93, N.255, L.257 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:W.92, A:R.93 Water bridges: A:W.92 EDO.12: 5 residues within 4Å: Chain A: Q.218, N.220, L.260, M.261 Ligands: K0I.1 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.260 Water bridges: A:Q.218, A:Q.218, A:E.219

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Walport, L.J. et al., Human Uty(Kdm6C) is a Male-Specific Nepislon-Methyl Lysyl Demethylase. J.Biol.Chem. (2014)

Release Date

2013-05-29

Peptides

HISTONE DEMETHYLASE UTY: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

HISTONE DEMETHYLASE UTY

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