SMTL ID : 5nuo.1

Structural basis for maintenance of bacterial outer membrane lipid asymmetry

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 3.20 Å

Oligo State

hetero-3-3-mer

Ligands

6 x SO4: SULFATE ION(Non-functional Binders)

SO4.1: 5 residues within 4Å: Chain A: T.165, R.167, R.168 Chain E: G.72, A.73 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain A Hydrogen bonds: E:A.73 Salt bridges: A:R.168 SO4.2: 4 residues within 4Å: Chain A: R.42, R.82, Y.102, R.132 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.42, A:R.82, A:R.132 SO4.12: 3 residues within 4Å: Chain C: R.42, R.82, R.132 3 PLIP interactions: 3 interactions with chain C Salt bridges: C:R.42, C:R.82, C:R.132 SO4.13: 5 residues within 4Å: Chain A: G.72, A.73 Chain C: T.165, R.167, R.168 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.165, A:A.73 Salt bridges: C:R.168 SO4.19: 5 residues within 4Å: Chain C: G.72, A.73 Chain E: T.165, R.167, R.168 2 PLIP interactions: 1 interactions with chain E, 1 interactions with chain C Salt bridges: E:R.168 Hydrogen bonds: C:A.73 SO4.20: 3 residues within 4Å: Chain E: R.42, R.82, R.132 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:R.42 Salt bridges: E:R.82, E:R.132

20 x C8E: (HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE(Non-functional Binders)

C8E.3: 6 residues within 4Å: Chain A: Y.263, F.265 Chain B: Y.79, M.82 Ligands: C8E.4, C8E.5 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.265 C8E.4: 5 residues within 4Å: Chain A: I.225, A.261, Y.263, I.273 Ligands: C8E.3 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:Y.263, A:I.273 Hydrogen bonds: A:Y.263 C8E.5: 6 residues within 4Å: Chain A: V.297, G.298, Y.313 Chain B: F.85 Ligands: C8E.3, C8E.7 5 PLIP interactions: 2 interactions with chain B, 3 interactions with chain A Hydrophobic interactions: B:F.85, B:F.85, A:V.297, A:V.297, A:Y.313 C8E.6: 10 residues within 4Å: Chain A: V.93, F.145 Chain F: P.51, A.52, N.54, G.55, N.58, L.99, D.101, M.105 8 PLIP interactions: 4 interactions with chain F, 4 interactions with chain A Hydrophobic interactions: F:A.52, F:L.99, A:V.93, A:F.145, A:F.145, A:F.145 Hydrogen bonds: F:N.58, F:D.101 C8E.7: 7 residues within 4Å: Chain A: F.23 Chain B: F.85, F.88, F.89, I.93 Ligands: C8E.5, C8E.14 No protein-ligand interaction detected (PLIP) C8E.8: 8 residues within 4Å: Chain B: P.51, N.54, G.55, N.58, L.99 Chain C: V.93, Y.139, F.145 4 PLIP interactions: 1 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.99, C:V.93, C:Y.139, C:F.145 C8E.9: 4 residues within 4Å: Chain B: L.122, V.127, G.128, G.130 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.122, B:V.127 C8E.10: 3 residues within 4Å: Chain B: Y.138, F.141, W.170 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.141 Hydrogen bonds: B:Y.138 C8E.11: 5 residues within 4Å: Chain B: N.28, L.37, F.137, W.170, G.174 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.171 C8E.14: 7 residues within 4Å: Chain A: F.23 Chain B: T.92, I.93, M.96, G.97 Chain C: Y.157 Ligands: C8E.7 No protein-ligand interaction detected (PLIP) C8E.15: 4 residues within 4Å: Chain C: V.174, G.176, Y.191 Ligands: C8E.17 No protein-ligand interaction detected (PLIP) C8E.16: 6 residues within 4Å: Chain C: I.225, Q.262, Y.263, P.271, I.273 Ligands: C8E.18 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:Y.263, C:P.271, C:I.273 C8E.17: 4 residues within 4Å: Chain C: Y.191, R.235, K.253 Ligands: C8E.15 No protein-ligand interaction detected (PLIP) C8E.18: 9 residues within 4Å: Chain C: Y.263, F.265, P.271, I.273 Chain D: P.78, Y.79, M.82, Q.109 Ligands: C8E.16 4 PLIP interactions: 2 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:P.271, C:I.273 Hydrogen bonds: D:Q.109, D:Q.109 C8E.21: 5 residues within 4Å: Chain E: V.297, G.298, Y.313 Chain F: M.82, F.85 No protein-ligand interaction detected (PLIP) C8E.22: 7 residues within 4Å: Chain A: Y.98, Y.157, L.158, D.172 Chain E: H.21, F.23, V.334 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:D.172 C8E.23: 4 residues within 4Å: Chain E: I.225, A.261, Y.263 Ligands: C8E.26 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:I.225, E:A.261, E:Y.263, E:Y.263 C8E.24: 4 residues within 4Å: Chain E: E.48, Y.58, K.89, S.142 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:K.89, E:S.95, E:S.142 C8E.25: 5 residues within 4Å: Chain A: Y.157 Chain F: T.92, I.93, M.96, G.97 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:I.93 C8E.26: 6 residues within 4Å: Chain E: Y.263, F.265 Chain F: P.78, Y.79, M.82 Ligands: C8E.23 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:Y.263, E:F.265, F:P.78

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abellon-Ruiz, J. et al., Structural basis for maintenance of bacterial outer membrane lipid asymmetry. Nat Microbiol (2017)

Release Date

2017-10-25

Peptides

Outer membrane protein F: ACE
ABC transporter permease: BDF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

C
A

E
E

B
D

D
B

F
F

Membrane

We predict this structure to be a membrane protein.
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Outer membrane protein F

ABC transporter permease

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