SMTL ID : 6ip0.1

Crystal structure of Arabidopsis thaliana JMJ13 catalytic domain in complex with AKG

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

monomer

Ligands

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

AKG.1: 12 residues within 4Å: Chain A: Y.194, F.202, H.205, E.207, S.213, N.215, K.223, W.225, H.300, A.312 Ligands: NI.2, SO4.15 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.225 Hydrogen bonds: A:S.213, A:N.215 Salt bridges: A:K.223, A:H.300

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

NI.2: 4 residues within 4Å: Chain A: H.205, E.207, H.300 Ligands: AKG.1 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.3: 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.4: 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

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

SO4.5: 4 residues within 4Å: Chain A: S.404, L.454, R.455, D.456 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.455 SO4.6: 7 residues within 4Å: Chain A: V.337, P.338, L.339, L.340, P.341, T.409, V.411 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:L.339 SO4.7: 6 residues within 4Å: Chain A: Y.407, I.410, F.423, N.425, Y.429, P.432 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.425 SO4.8: 2 residues within 4Å: Chain A: R.100 Ligands: SO4.9 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.100 SO4.9: 4 residues within 4Å: Chain A: R.100, K.104 Ligands: SO4.8, SO4.12 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.100, A:K.104 SO4.10: 5 residues within 4Å: Chain A: R.100, K.104, N.107, K.108 Ligands: SO4.12 1 PLIP interactions: 1 interactions with chain A Salt bridges: A:R.100 SO4.11: 2 residues within 4Å: Chain A: K.65, S.66 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.66 Water bridges: A:K.65, A:K.65 Salt bridges: A:K.65 SO4.12: 4 residues within 4Å: Chain A: K.104, K.108 Ligands: SO4.9, SO4.10 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:K.104, A:K.108 SO4.13: 2 residues within 4Å: Chain A: F.323, I.326 No protein-ligand interaction detected (PLIP) SO4.14: 3 residues within 4Å: Chain A: K.69, T.96, T.98 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.96 Water bridges: A:T.98, A:T.98 Salt bridges: A:K.69 SO4.15: 9 residues within 4Å: Chain A: Y.143, Y.194, I.195, G.196, S.200, M.201, K.223, S.304 Ligands: AKG.1 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:M.201 Salt bridges: A:K.223 SO4.16: 3 residues within 4Å: Chain A: A.258, F.259, R.330 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:F.259 Salt bridges: A:K.241, A:R.330 SO4.17: 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

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

Transcription factor jumonji (Jmj) family protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Transcription factor jumonji (Jmj) family protein

Related Entries With Identical Sequence