SMTL ID : 6ip4.1

Crystal structure of Arabidopsis thaliana JMJ13 catalytic domain in complex with NOG and an H3K27me3 peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.60 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.205, E.207, H.300 Ligands: OGA.4 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.205, A:E.207, A:H.300, H2O.1

2 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.412, C.415, C.434, H.437 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.412, A:C.415, A:C.434, A:H.437 ZN.3: 5 residues within 4Å: Chain A: C.426, C.428, S.430, H.431, C.446 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.426, A:C.428, A:H.431, A:C.446

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

OGA.4: 13 residues within 4Å: Chain A: Y.143, Y.194, F.202, H.205, E.207, S.213, N.215, K.223, W.225, H.300, A.312 Chain B: K.4 Ligands: NI.1 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:Y.143, A:S.213, A:N.215 Salt bridges: A:K.223, A:H.300

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.5: 5 residues within 4Å: Chain A: L.402, S.404, L.454, R.455, D.456 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.455 SO4.6: 6 residues within 4Å: Chain A: P.338, L.339, L.340, P.341, T.409, V.411 No protein-ligand interaction detected (PLIP) SO4.7: 2 residues within 4Å: Chain A: N.107, K.108 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.104 SO4.8: 2 residues within 4Å: Chain A: K.65, S.66 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:S.66 SO4.9: 3 residues within 4Å: Chain A: P.322, F.323, I.326 No protein-ligand interaction detected (PLIP) SO4.10: 2 residues within 4Å: Chain A: H.437, D.438 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:D.438 Salt bridges: A:H.437 SO4.11: 2 residues within 4Å: Chain A: R.100, K.104 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.100

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zheng, S. et al., The Arabidopsis H3K27me3 demethylase JUMONJI 13 is a temperature and photoperiod dependent flowering repressor. Nat Commun (2019)

Release Date

2019-04-10

Peptides

Arabidopsis JMJ13: A
Histone H3.2: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Arabidopsis JMJ13

Histone H3.2

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