SMTL ID : 6f4s.1

Human JMJD5 (N308C) in complex with Mn(II), 2OG and RCCD1 (139-143) (complex-4)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.46 Å

Oligo State

monomer

Ligands

1 x CYS- ALA- ARG- ALA- TYR: RCC1 domain-containing protein 1(Non-covalent)

CYS-ALA-ARG-ALA-TYR.1: 19 residues within 4Å: Chain A: E.77, Y.82, W.87, Y.111, A.113, Q.114, T.145, C.147, W.149, I.156, S.157, H.160, D.162, L.195, N.198, S.251, W.253 Ligands: MN.2, AKG.3 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:Y.82, A:Y.82 Hydrogen bonds: A:E.77, A:E.77, A:Q.114, A:Q.114, A:Q.114, A:S.157, A:N.198 Water bridges: A:E.77, A:T.145

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

MN.2: 6 residues within 4Å: Chain A: H.160, D.162, H.239, W.253 Ligands: CYS-ALA-ARG-ALA-TYR.1, AKG.3 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 AKG: 2-OXOGLUTARIC ACID(Non-covalent)

AKG.3: 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 Ligands: CYS-ALA-ARG-ALA-TYR.1, MN.2 11 PLIP interactions: 11 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, A:S.251, A:W.253 Water bridges: A:S.157 Salt bridges: A:K.175, A:H.239

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

TRS.4: 7 residues within 4Å: Chain A: L.39, V.40, P.41, G.42, Q.165, P.234, V.235 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:L.39, A:Q.165 Water bridges: A:V.40, A:V.235, A:V.235

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 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, A:D.132 Water bridges: A:D.132

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