SMTL ID : 3kv6.3 (2 other biounits)

Structure of KIAA1718, human Jumonji demethylase, in complex with alpha-ketoglutarate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.89 Å

Oligo State

homo-dimer

Ligands

4 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: C.55, C.58, C.82, C.85 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.55, A:C.58, A:C.82, A:C.85 ZN.2: 4 residues within 4Å: Chain A: C.40, C.42, H.63, C.66 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.40, A:C.42, A:H.63, A:C.66 ZN.6: 4 residues within 4Å: Chain B: C.55, C.58, C.82, C.85 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.55, B:C.58, B:C.82, B:C.85 ZN.7: 4 residues within 4Å: Chain B: C.40, C.42, H.63, C.66 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.40, B:C.42, B:H.63, B:C.66

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

FE2.3: 5 residues within 4Å: Chain A: H.282, D.284, Y.292, H.354 Ligands: AKG.5 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.282, A:D.284, A:H.354 FE2.8: 4 residues within 4Å: Chain B: H.282, D.284, H.354 Ligands: AKG.10 3 PLIP interactions: 3 interactions with chain B Metal complexes: B:H.282, B:D.284, B:H.354

2 x OXY: OXYGEN MOLECULE(Non-covalent)

OXY.4: 4 residues within 4Å: Chain A: Y.269, Y.292, N.368 Ligands: AKG.5 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.292 OXY.9: 3 residues within 4Å: Chain B: Y.269, N.368 Ligands: AKG.10 No protein-ligand interaction detected (PLIP)

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

AKG.5: 11 residues within 4Å: Chain A: N.224, I.226, T.279, H.282, D.284, Y.292, K.299, V.356, T.358 Ligands: FE2.3, OXY.4 6 PLIP interactions: 6 interactions with chain A Hydrophobic interactions: A:I.226, A:V.356 Hydrogen bonds: A:N.224, A:Y.292 Salt bridges: A:H.282, A:K.299 AKG.10: 12 residues within 4Å: Chain B: I.226, L.271, T.279, H.282, D.284, Y.292, K.299, H.354, V.356, T.358 Ligands: FE2.8, OXY.9 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:V.356 Hydrogen bonds: B:T.279, B:T.279 Salt bridges: B:H.282, B:K.299

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
D

JmjC domain-containing histone demethylation protein 1D

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