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

Structure of KIAA1718 Jumonji domain in complex with alpha-ketoglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

homo-dimer

Ligands

4 x FE2: FE (II) ION(Non-covalent)

FE2.1: 4 residues within 4Å: Chain A: H.191, D.193, H.263 Ligands: AKG.4 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:H.191, A:D.193, A:D.193, A:H.263 FE2.2: 5 residues within 4Å: Chain A: S.158, W.159, V.160, F.278, L.279 No protein-ligand interaction detected (PLIP) FE2.5: 4 residues within 4Å: Chain B: H.191, D.193, H.263 Ligands: AKG.8 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:H.191, B:D.193, B:D.193, B:H.263 FE2.6: 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: 3 residues within 4Å: Chain A: I.135, Y.178, N.277 No protein-ligand interaction detected (PLIP) OXY.7: 3 residues within 4Å: Chain B: I.135, Y.178, N.277 No protein-ligand interaction detected (PLIP)

2 x AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.4: 12 residues within 4Å: Chain A: N.133, I.135, L.180, T.188, H.191, D.193, V.199, Y.201, K.208, H.263, V.265 Ligands: FE2.1 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: A:L.180, A:Y.201, A:V.265 Hydrogen bonds: A:N.133, A:T.188, A:T.188 Salt bridges: A:K.208, A:H.263 AKG.8: 12 residues within 4Å: Chain B: N.133, I.135, L.180, T.188, H.191, D.193, V.199, Y.201, K.208, H.263, V.265 Ligands: FE2.5 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:L.180, B:Y.201, B:V.265 Hydrogen bonds: B:N.133, B:T.188, B:T.188, B:Y.201 Salt bridges: B:K.208, B:H.263

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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