SMTL ID : 4r0c.1

Crystal structure of the Alcanivorax borkumensis YdaH transporter reveals an unusual topology

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.96 Å

Oligo State

homo-tetramer

Ligands

4 x NA: SODIUM ION(Non-functional Binders)

NA.1: 5 residues within 4Å: Chain A: N.390, G.394, K.399, D.429, N.433 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.390, A:K.399, A:K.399, A:N.433 NA.7: 5 residues within 4Å: Chain B: N.390, G.394, K.399, D.429, N.433 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.390, B:N.390, B:K.399, B:N.433 NA.8: 5 residues within 4Å: Chain C: N.390, G.394, K.399, D.429, N.433 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.390, C:K.399, C:D.429, C:N.433 NA.13: 5 residues within 4Å: Chain D: N.390, G.394, K.399, D.429, N.433 4 PLIP interactions: 4 interactions with chain D Hydrogen bonds: D:N.390, D:N.390, D:K.399, D:N.433

6 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)

LMT.2: 7 residues within 4Å: Chain A: S.105, L.106, S.108, R.112, I.248, M.253 Ligands: BOG.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.106 Hydrogen bonds: A:R.112 Salt bridges: A:R.112 LMT.4: 6 residues within 4Å: Chain A: Y.206, L.267, V.286, L.287, F.291, I.292 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:Y.206, A:L.267, A:V.286, A:F.291, A:I.292 LMT.5: 6 residues within 4Å: Chain A: H.249, R.251, W.255, T.259, V.313, S.314 7 PLIP interactions: 7 interactions with chain A Hydrophobic interactions: A:W.255, A:W.255, A:W.255 Hydrogen bonds: A:H.249, A:R.251, A:V.313 Salt bridges: A:R.251 LMT.6: 7 residues within 4Å: Chain A: V.88, L.91, G.92, L.301, S.320, V.323 Chain B: V.26 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.26, A:L.91, A:L.301 LMT.10: 9 residues within 4Å: Chain C: L.102, S.105, L.106, S.108, L.109, R.112, T.132, M.253 Ligands: BOG.11 6 PLIP interactions: 6 interactions with chain C Hydrophobic interactions: C:L.102, C:L.106, C:L.109, C:T.132 Hydrogen bonds: C:R.112, C:R.112 LMT.12: 9 residues within 4Å: Chain C: V.88, G.92, V.95, V.297, L.301, G.304, V.323 Chain D: L.23, V.26 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:V.95, C:V.297, C:L.301, C:V.323

4 x BOG: octyl beta-D-glucopyranoside(Non-covalent)

BOG.3: 4 residues within 4Å: Chain A: L.101, S.105, G.257 Ligands: LMT.2 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:L.101 BOG.9: 1 residues within 4Å: Chain C: R.112 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:R.112 BOG.11: 4 residues within 4Å: Chain C: M.253, G.257, L.260 Ligands: LMT.10 No protein-ligand interaction detected (PLIP) BOG.14: 13 residues within 4Å: Chain C: V.85, H.293, G.294, V.297, I.298, L.301 Chain D: L.69, F.70, T.71, T.72, L.73, V.74, G.75 13 PLIP interactions: 4 interactions with chain C, 9 interactions with chain D Hydrophobic interactions: C:V.297, C:I.298, C:L.301, D:F.70, D:F.70, D:L.73, D:L.73 Hydrogen bonds: C:V.297, D:L.69, D:T.71, D:L.73, D:V.74, D:G.75

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Bolla, J.R. et al., Crystal structure of the Alcanivorax borkumensis YdaH transporter reveals an unusual topology. Nat Commun (2015)

Release Date

2015-04-29

Peptides

AbgT putative transporter family: ABCD

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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AbgT putative transporter family