SMTL ID : 4liu.1

Structure of YcfD, a Ribosomal oxygenase from Escherichia coli.

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-dimer

Ligands

2 x TAM: TRIS(HYDROXYETHYL)AMINOMETHANE(Non-covalent)

TAM.1: 3 residues within 4Å: Chain A: E.335, E.406, G.407 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.406 TAM.3: 3 residues within 4Å: Chain B: E.335, E.406, G.407 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:E.406 Hydrogen bonds: B:G.407

2 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.2: 6 residues within 4Å: Chain A: L.116, M.146, S.148, R.174, W.176, N.231 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:S.148 Water bridges: A:S.148, A:R.174, A:R.174, A:S.233, A:S.233, A:S.233 Salt bridges: A:R.174 PO4.4: 6 residues within 4Å: Chain B: L.116, M.146, S.148, R.174, W.176, N.231 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:S.148 Water bridges: B:S.148, B:R.174, B:R.174, B:S.233, B:S.233, B:S.233 Salt bridges: B:R.174

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chowdhury, R. et al., Ribosomal oxygenases are structurally conserved from prokaryotes to humans. Nature (2014)

Release Date

2014-05-14

Peptides

50S ribosomal protein L16 arginine hydroxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

50S ribosomal protein L16 arginine hydroxylase

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