SMTL ID : 6f4o.1

Human JMJD5 in complex with Mn(II) and Succinate.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.28 Å

Oligo State

monomer

Ligands

1 x MN: MANGANESE (II) ION(Non-covalent)

MN.1: 5 residues within 4Å: Chain A: H.160, D.162, H.239, W.253 Ligands: SIN.2 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:H.160, A:D.162, A:H.239, H2O.4

1 x SIN: SUCCINIC ACID(Non-covalent)

SIN.2: 12 residues within 4Å: Chain A: Y.111, W.149, S.157, H.160, D.162, N.166, L.168, K.175, H.239, V.241, W.253 Ligands: MN.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:W.149, A:W.149, A:V.241 Hydrogen bonds: A:Y.111, A:S.157, A:N.166 Water bridges: A:W.149, A:S.157, A:W.253 Salt bridges: A:H.160, A:K.175, A:H.239

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.3: 7 residues within 4Å: Chain A: L.39, V.40, P.41, G.42, Q.165, P.234, V.235 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.165 Water bridges: A:V.235, A:V.235

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Wilkins, S.E. et al., JMJD5 is a human arginyl C-3 hydroxylase. Nat Commun (2018)

Release Date

2018-04-04

Peptides

JmjC domain-containing protein 5: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

JmjC domain-containing protein 5