SMTL ID : 4r9u.1

Structure of vitamin B12 transporter BtuCD in a nucleotide-bound outward facing state

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.79 Å

Oligo State

hetero-2-2-mer

Ligands

4 x LDA: LAURYL DIMETHYLAMINE-N-OXIDE(Non-covalent)

LDA.1: 4 residues within 4Å: Chain A: W.122, L.126, R.196, W.199 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:W.122, A:W.122, A:L.126, A:W.199, A:W.199 LDA.2: 1 residues within 4Å: Chain A: W.195 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:W.195 pi-Cation interactions: A:W.195 LDA.3: 3 residues within 4Å: Chain B: W.122, L.126, W.199 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:W.122, B:W.122, B:L.126, B:W.199, B:W.199 LDA.4: 2 residues within 4Å: Chain B: W.60, W.195 2 PLIP interactions: 2 interactions with chain B pi-Cation interactions: B:W.195, B:W.195

2 x ANP: PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER(Non-covalent)

ANP.5: 19 residues within 4Å: Chain C: R.15, N.35, G.36, G.38, K.39, S.40, T.41, Q.80, Q.159, H.191 Chain D: R.122, Q.126, L.127, S.128, G.129, G.130, E.131, S.163 Ligands: MG.6 24 PLIP interactions: 17 interactions with chain C, 7 interactions with chain D Hydrogen bonds: C:R.15, C:G.36, C:G.36, C:A.37, C:G.38, C:K.39, C:K.39, C:K.39, C:S.40, C:S.40, C:T.41, C:T.41, C:Q.80, C:Q.80, C:Q.159, D:R.122, D:R.122, D:S.128, D:G.129, D:G.130, D:E.131, D:S.163 pi-Cation interactions: C:R.15, C:R.15 ANP.7: 21 residues within 4Å: Chain C: R.122, Q.126, L.127, S.128, G.129, G.130, E.131, S.163 Chain D: R.15, P.34, N.35, G.36, A.37, G.38, K.39, S.40, T.41, Q.80, Q.159, H.191 Ligands: MG.8 19 PLIP interactions: 12 interactions with chain D, 7 interactions with chain C Hydrogen bonds: D:P.34, D:G.36, D:A.37, D:G.38, D:K.39, D:K.39, D:S.40, D:S.40, D:T.41, D:Q.80, C:R.122, C:R.122, C:S.128, C:G.129, C:G.130, C:E.131, C:S.163 pi-Cation interactions: D:R.15, D:R.15

2 x MG: MAGNESIUM ION(Non-covalent)

MG.6: 4 residues within 4Å: Chain C: S.40, Q.80, Q.159 Ligands: ANP.5 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:S.40 MG.8: 3 residues within 4Å: Chain D: S.40, Q.80 Ligands: ANP.7 1 PLIP interactions: 1 interactions with chain D Metal complexes: D:S.40

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Korkhov, V.M. et al., Structure of AMP-PNP-bound BtuCD and mechanism of ATP-powered vitamin B12 transport by BtuCD-F. Nat.Struct.Mol.Biol. (2014)

Release Date

2014-11-19

Peptides

Vitamin B12 import system permease protein BtuC: AB
Vitamin B12 import ATP-binding protein BtuD: CD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Membrane

We predict this structure to be a membrane protein.
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Vitamin B12 import system permease protein BtuC

Vitamin B12 import ATP-binding protein BtuD

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