SMTL ID : 3kvb.2 (1 other biounit)

Structure of KIAA1718 Jumonji domain in complex with N-oxalylglycine

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.69 Å

Oligo State

homo-dimer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: H.191, D.193, H.263 Ligands: OGA.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.191, A:D.193, A:H.263 NI.2: 5 residues within 4Å: Chain A: S.158, W.159, V.160, F.278, L.279 No protein-ligand interaction detected (PLIP) NI.5: 4 residues within 4Å: Chain B: H.191, D.193, H.263 Ligands: OGA.8 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.191, B:D.193, B:H.263 NI.6: 5 residues within 4Å: Chain B: S.158, W.159, V.160, F.278, L.279 No protein-ligand interaction detected (PLIP)

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.3: 2 residues within 4Å: Chain A: V.199, N.277 No protein-ligand interaction detected (PLIP) OXY.7: 2 residues within 4Å: Chain B: V.199, N.277 No protein-ligand interaction detected (PLIP)

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

OGA.4: 10 residues within 4Å: Chain A: N.133, I.135, T.188, H.191, D.193, Y.201, K.208, H.263, V.265 Ligands: NI.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:N.133, A:Y.201 Water bridges: A:K.208 Salt bridges: A:H.191, A:K.208 OGA.8: 10 residues within 4Å: Chain B: N.133, I.135, T.188, H.191, D.193, Y.201, K.208, H.263, V.265 Ligands: NI.5 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.133, B:T.188, B:Y.201, B:Y.201 Water bridges: B:K.208 Salt bridges: B:H.191, B:K.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Horton, J.R. et al., Enzymatic and structural insights for substrate specificity of a family of jumonji histone lysine demethylases. Nat.Struct.Mol.Biol. (2010)

Release Date

2009-12-22

Peptides

JmjC domain-containing histone demethylation protein 1D: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

JmjC domain-containing histone demethylation protein 1D

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