SMTL ID : 3uyj.1

Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.35 Å

Oligo State

homo-dimer

Ligands

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

NI.1: 4 residues within 4Å: Chain A: H.153, D.155, H.232 Ligands: AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.153, A:D.155, A:H.232, H2O.4 NI.3: 4 residues within 4Å: Chain B: H.153, D.155, H.232 Ligands: AKG.4 4 PLIP interactions: 3 interactions with chain B, 1 Ligand-Water interactions Metal complexes: B:H.153, B:D.155, B:H.232, H2O.136

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

AKG.2: 13 residues within 4Å: Chain A: Y.104, W.142, S.150, H.153, D.155, N.159, L.161, K.168, H.232, V.234, S.244, W.246 Ligands: NI.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.142, A:W.142, A:V.234 Hydrogen bonds: A:Y.104, A:S.150, A:S.150, A:N.159, A:S.244 Water bridges: A:S.150 Salt bridges: A:K.168, A:H.232 AKG.4: 13 residues within 4Å: Chain B: Y.104, W.142, S.150, H.153, D.155, N.159, L.161, K.168, H.232, V.234, S.244, W.246 Ligands: NI.3 9 PLIP interactions: 9 interactions with chain B Hydrophobic interactions: B:W.142, B:W.142 Hydrogen bonds: B:S.150, B:S.150, B:N.159, B:S.244 Water bridges: B:S.150 Salt bridges: B:K.168, B:H.232

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Su, X. et al., Crystal structure of JMJD5 catalytic core domain in complex with nickle and alpha-KG. To be Published

Release Date

2011-12-21

Peptides

Lysine-specific demethylase 8: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Lysine-specific demethylase 8