SMTL ID : 6f4p.1

Human JMJD5 in complex with MN, NOG and RPS6 (129-144) (complex-1)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.45 Å

Oligo State

hetero-1-1-mer

Ligands

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

MN.1: 6 residues within 4Å: Chain A: H.160, D.162, H.239, W.253 Chain B: R.3 Ligands: OGA.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.6

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

OGA.2: 14 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, W.253 Chain B: R.3 Ligands: MN.1 9 PLIP interactions: 9 interactions with chain A Hydrogen bonds: A:Y.111, A:S.157, A:N.166, A:W.253 Water bridges: A:W.149, A:S.157, A:H.160 Salt bridges: 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 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:L.39, 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
40S ribosomal protein S6: B

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

JmjC domain-containing protein 5

40S ribosomal protein S6