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

CEKDM7A from C.Elegans, complex with alpha-KG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

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

FE2.1: 4 residues within 4Å: Chain A: H.312, D.314, H.384 Ligands: AKG.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.312, A:D.314, A:H.384, H2O.1

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.15, C.18, H.69, C.72 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.15, A:C.18, A:C.72 ZN.3: 4 residues within 4Å: Chain A: C.61, C.64, C.88, C.91 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.61, A:C.64, A:C.88, A:C.91

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

AKG.4: 11 residues within 4Å: Chain A: N.238, L.240, T.309, H.312, D.314, Y.322, K.329, F.331, H.384, V.386 Ligands: FE2.1 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:L.240, A:T.309, A:V.386 Hydrogen bonds: A:T.309, A:Y.322 Water bridges: A:T.309, A:K.329 Salt bridges: A:H.312, A:K.329

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 3 residues within 4Å: Chain A: H.312, D.314, F.315 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:F.315

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Xu, W. et al., Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of alpha-ketoglutarate-dependent dioxygenases. Cancer Cell (2011)

Release Date

2011-01-26

Peptides

Lysine-specific demethylase 7 homolog: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

Lysine-specific demethylase 7 homolog

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