SMTL ID : 6f4t.1

Human JMJD5 (W414C) in complex with Mn(II), NOG and RCCD1 (139-143) (complex-5)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.22 Å

Oligo State

monomer

Ligands

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

MN.1: 4 residues within 4Å: Chain A: H.160, D.162, H.239 Ligands: OGA.2 3 PLIP interactions: 3 interactions with chain A Metal complexes: A:H.160, A:D.162, A:H.239

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

OGA.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, S.251 Ligands: MN.1 10 PLIP interactions: 10 interactions with chain A Hydrogen bonds: A:Y.111, A:S.157, A:N.166, A:S.251 Water bridges: A:W.149, A:W.149, A:S.157, A:H.160 Salt bridges: A:K.175, A:H.239

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 7 residues within 4Å: Chain A: R.28, P.29, S.30, L.31, V.50, D.132, Y.133 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.28, A:R.28, A:L.31, A:D.132, A:D.132 Water bridges: A:P.29, A:D.132 GOL.4: 4 residues within 4Å: Chain A: R.174, I.224, R.242, L.244 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.174, A:R.174 GOL.5: 3 residues within 4Å: Chain A: N.95, E.96, S.99 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.99 Water bridges: A:N.95, A:S.99, A:S.99

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

TRS.6: 7 residues within 4Å: Chain A: L.39, V.40, P.41, G.42, Q.165, P.234, V.235 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.165 Water bridges: A:V.40, 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