SMTL ID : 5m34.2 (1 other biounit)

Structure of cobinamide-bound BtuF mutant W66Y, the periplasmic vitamin B12 binding protein in E.coli

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.60 Å

Oligo State

monomer

Ligands

2 x CYN: CYANIDE ION(Non-covalent)

CYN.1: 4 residues within 4Å: Chain A: Y.69, W.88 Ligands: CBY.2, CYN.3 No protein-ligand interaction detected (PLIP) CYN.3: 3 residues within 4Å: Chain A: E.248 Ligands: CYN.1, CBY.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.248 Water bridges: A:T.218

1 x CBY: COB(II)INAMIDE(Non-covalent)

CBY.2: 17 residues within 4Å: Chain A: S.33, P.34, A.35, Y.53, Y.69, W.88, G.90, F.165, F.171, Q.179, W.199, D.245, E.248, R.249 Ligands: CYN.1, CYN.3, GOL.4 27 PLIP interactions: 27 interactions with chain A, Hydrophobic interactions: A:P.34, A:Y.53, A:Y.53, A:Y.69, A:W.88, A:F.165, A:F.171, A:F.171, A:W.199, A:W.199, A:W.199, A:W.199, A:E.248, A:E.248 Hydrogen bonds: A:S.33, A:S.33, A:A.35, A:Y.69, A:W.199, A:D.245, A:D.245, A:R.249 Water bridges: A:N.36, A:S.52, A:S.52, A:N.168, A:A.250

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 9 residues within 4Å: Chain A: P.34, S.51, S.52, Y.53, S.67, T.68, Y.69, W.88 Ligands: CBY.2 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.52, A:S.67 Water bridges: A:S.52

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mireku, S.A. et al., Conformational Change of a Tryptophan Residue in BtuF Facilitates Binding and Transport of Cobinamide by the Vitamin B12 Transporter BtuCD-F. Sci Rep (2017)

Release Date

2017-03-01

Peptides

Vitamin B12-binding protein: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

Vitamin B12-binding protein

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