SMTL ID : 5yko.1

Crystal structure of Arabidopsis thaliana JMJ14 catalytic domain in complex with NOG and H3K4me3 peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-1-1-mer

Ligands

1 x NI: NICKEL (II) ION(Non-covalent)

NI.1: 4 residues within 4Å: Chain A: H.276, E.278, H.364 Ligands: OGA.4 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.276, A:E.278, A:H.364

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.486, C.489, C.509, H.512 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.486, A:C.489, A:C.509, A:H.512 ZN.3: 4 residues within 4Å: Chain A: C.500, C.502, C.517, C.519 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:C.500, A:C.502, A:C.517

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

OGA.4: 13 residues within 4Å: Chain A: Y.203, Y.265, F.273, H.276, E.278, S.284, N.286, K.294, W.296, H.364, A.376 Chain B: K.4 Ligands: NI.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.203, A:S.284, A:N.286 Salt bridges: A:K.294, A:H.364

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Yang, Z. et al., Structure of the Arabidopsis JMJ14-H3K4me3 Complex Provides Insight into the Substrate Specificity of KDM5 Subfamily Histone Demethylases. Plant Cell (2018)

Release Date

2017-12-27

Peptides

Probable lysine-specific demethylase JMJ14: A
H3(1-10)K4me3 peptide: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
P

Probable lysine-specific demethylase JMJ14

H3(1-10)K4me3 peptide

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