SMTL ID : 6ax3.1

Complex structure of JMJD5 and Symmetric Dimethyl-Arginine (SDMA)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.25 Å

Oligo State

monomer

Ligands

1 x 2MR: N3, N4-DIMETHYLARGININE(Non-covalent)

2MR.1: 10 residues within 4Å: Chain A: E.58, Q.95, W.130, I.137, S.138, H.141, D.143, W.234 Ligands: AKG.2, ZN.3 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.130 Hydrogen bonds: A:Q.95, A:Q.95 Water bridges: A:Q.142 Salt bridges: A:H.141

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

AKG.2: 14 residues within 4Å: Chain A: Y.92, W.130, S.138, H.141, D.143, N.147, L.149, K.156, H.220, V.222, S.232, W.234 Ligands: 2MR.1, ZN.3 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:W.130, A:V.222 Hydrogen bonds: A:S.138, A:S.138, A:N.147, A:S.232 Water bridges: A:S.138 Salt bridges: A:K.156, A:H.220

1 x ZN: ZINC ION(Non-covalent)

ZN.3: 5 residues within 4Å: Chain A: H.141, D.143, H.220 Ligands: 2MR.1, AKG.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Ligand interactions Metal complexes: A:H.141, A:D.143, A:H.220, 2MR.1

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Liu, H. et al., Specific Recognition of Arginine Methylated Histone Tails by JMJD5 and JMJD7. Sci Rep (2018)

Release Date

2018-02-28

Peptides

Lysine-specific demethylase 8: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

Lysine-specific demethylase 8