SMTL ID : 3n9o.1

ceKDM7A from C.elegans, complex with H3K4me3 peptide, H3K9me2 peptide and NOG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.31 Å

Oligo State

hetero-1-1-1-mer

Ligands

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

FE2.1: 4 residues within 4Å: Chain A: H.312, D.314, H.384 Ligands: OGA.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: 5 residues within 4Å: Chain A: C.15, C.18, H.23, H.69, C.72 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.15, A:C.18, A:H.69, 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 OGA: N-OXALYLGLYCINE(Non-covalent)

OGA.4: 13 residues within 4Å: Chain A: N.238, L.240, L.301, T.309, H.312, D.314, V.320, Y.322, K.329, H.384, V.386 Chain C: K.9 Ligands: FE2.1 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.238, A:T.309, A:T.309 Water bridges: A:K.329, A:T.388 Salt bridges: A:K.329, A:H.384

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Y. et al., Structural insights into a dual-specificity histone demethylase ceKDM7A from Caenorhabditis elegans. Cell Res. (2010)

Release Date

2010-06-30

Peptides

Putative uncharacterized protein: A
Histone H3 peptide: B
Histone H3 peptide: C

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

Putative uncharacterized protein

Histone H3 peptide

Histone H3 peptide

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