SMTL ID : 6hgt.4 (3 other biounits)

Crystal structure of human KDM4A complexed with co-substrate analog NOG and histone H3 peptide with K9R mutation

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.33 Å

Oligo State

hetero-1-1-mer

Ligands

2 x ZN: ZINC ION(Non-covalent)

ZN.1: 4 residues within 4Å: Chain A: H.189, E.191, H.277 Ligands: OGA.3 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.189, A:E.191, A:H.277 ZN.2: 5 residues within 4Å: Chain A: C.235, H.241, C.307, S.308, C.309 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.235, A:H.241, A:C.307, A:C.309

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

OGA.3: 12 residues within 4Å: Chain A: Y.133, F.186, H.189, E.191, S.197, N.199, K.207, W.209, H.277, S.289 Chain B: R.7 Ligands: ZN.1 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Y.133, A:S.197, A:N.199, A:S.289 Salt bridges: A:K.207, A:H.277, B:R.7

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Maw, J. et al., Structure-based design of selective, histone substrate-based inhibitors of histone lysine demethylases 4 (KDM4) subfamily. To be published

Release Date

2019-09-04

Peptides

Lysine-specific demethylase 4A: A
Histone H3.3: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
D

B
H

Lysine-specific demethylase 4A

Histone H3.3

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