SMTL ID : 3avr.1

Catalytic fragment of UTX/KDM6A bound with histone H3K27me3 peptide, N-oxyalylglycine, and Ni(II)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

hetero-1-1-mer

Ligands

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

OGA.1: 16 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 Chain B: K.11 Ligands: NI.3 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: 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

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

NI.3: 6 residues within 4Å: Chain A: H.276, E.278, S.284, H.356 Chain B: K.11 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.10

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

EDO.4: 5 residues within 4Å: Chain A: V.243, S.244, A.245, S.250, H.251 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.250 EDO.5: 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.6: 2 residues within 4Å: Chain A: M.127, H.159 No protein-ligand interaction detected (PLIP) EDO.7: 3 residues within 4Å: Chain A: I.19, Y.20, P.21 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.20 EDO.8: 8 residues within 4Å: Chain A: T.116, A.166, Q.169, A.170, F.173, P.291, W.363, C.364 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.116, A:T.116 EDO.9: 7 residues within 4Å: Chain A: V.130, T.160, T.161, K.164, Y.165, Y.168, K.213 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.213 EDO.10: 5 residues within 4Å: Chain A: F.82, P.237, A.238, F.239, R.241 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:A.238, A:R.241, A:R.241 Water bridges: A:F.239 EDO.11: 11 residues within 4Å: Chain A: T.91, P.93, C.283, W.349, N.351, A.352, P.373, T.375, C.377, Q.378, L.381 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.351 Water bridges: A:A.352 EDO.12: 7 residues within 4Å: Chain A: L.111, G.112, F.114, S.115, I.289, G.290, P.291 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.111, A:G.290

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

CL.13: 3 residues within 4Å: Chain A: R.452, K.454, E.455 Ligand excluded by PLIP CL.14: 3 residues within 4Å: Chain A: R.241, S.244, A.245 Ligand excluded by PLIP

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
Histone H3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine-specific demethylase 6A

Histone H3

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