SMTL ID : 3avs.1

Catalytic fragment of UTX/KDM6A bound with N-oxyalylglycine, and Ni(II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

monomer

Ligands

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

OGA.1: 15 residues within 4Å: Chain A: F.214, Y.265, K.267, T.273, H.276, E.278, S.284, N.286, W.296, I.350, H.356, V.358, N.366, A.368 Ligands: NI.3 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.265, A:T.273, A:S.284, A:N.286 Water bridges: A:T.273 Salt bridges: A:K.267, A:H.356

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 6 residues within 4Å: Chain A: C.461, I.463, C.464, V.466, C.488, C.491 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.461, A:C.464, A:C.488, A:C.491

3 x NI: NICKEL (II) ION(Non-covalent)

NI.3: 5 residues within 4Å: Chain A: H.276, E.278, S.284, H.356 Ligands: OGA.1 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.276, A:E.278, A:H.356, H2O.11 NI.4: 2 residues within 4Å: Chain A: H.450, E.456 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.450 NI.5: 1 residues within 4Å: Chain A: H.231 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:H.231

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.6: 1 residues within 4Å: Chain A: R.157 Ligand excluded by PLIP

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

EDO.7: 7 residues within 4Å: Chain A: V.243, S.244, A.245, S.250, H.251, N.410 Ligands: EDO.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.250 EDO.8: 10 residues within 4Å: Chain A: Y.379, V.383, Y.386, E.387, M.400, V.401, S.404, C.425, R.428, T.429 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:E.387, A:S.404, A:R.428, A:R.428 EDO.9: 1 residues within 4Å: Chain A: Y.58 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.58 EDO.10: 7 residues within 4Å: Chain A: V.130, S.158, T.160, K.164, Y.165, Y.168, K.213 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.160, A:K.164, A:K.213 Water bridges: A:Y.168 EDO.11: 4 residues within 4Å: Chain A: G.102, R.343, P.344, G.345 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:P.344 Water bridges: A:G.102 EDO.12: 6 residues within 4Å: Chain A: Y.379, K.380, V.383, E.384, M.421, Y.424 No protein-ligand interaction detected (PLIP) EDO.13: 7 residues within 4Å: Chain A: L.111, G.112, S.115, I.289, G.290, P.291 Ligands: EDO.14 No protein-ligand interaction detected (PLIP) EDO.14: 11 residues within 4Å: Chain A: S.115, T.116, K.117, Q.169, I.289, G.290, P.291, W.363, C.364, N.365 Ligands: EDO.13 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:T.116, A:Q.169, A:C.364, A:N.365 Water bridges: A:K.117 EDO.15: 7 residues within 4Å: Chain A: P.69, T.70, S.72, Y.74, R.101, F.340, I.341 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.101 EDO.16: 6 residues within 4Å: Chain A: A.238, R.241, V.243, S.244, A.245 Ligands: EDO.7 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.241, A:A.245

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sengoku, T. et al., Structural basis for histone H3 Lys 27 demethylation by UTX/KDM6A. Genes Dev. (2011)

Release Date

2011-10-19

Peptides

Lysine-specific demethylase 6A: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 6A

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