SMTL ID : 5nup.1

Structural basis for maintenance of bacterial outer membrane lipid asymmetry

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.90 Å

Oligo State

hetero-3-3-mer

Ligands

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

C8E.1: 7 residues within 4Å: Chain A: Y.263, F.265 Chain D: P.78, Y.79, M.82 Ligands: C8E.4, C8E.17 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:F.265, D:Y.79 C8E.2: 3 residues within 4Å: Chain A: Q.238, K.253, Q.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.255 C8E.3: 5 residues within 4Å: Chain A: Y.219, G.221, Y.236, Q.238, Y.240 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.236, A:Q.238 C8E.4: 2 residues within 4Å: Chain A: Y.263 Ligands: C8E.1 No protein-ligand interaction detected (PLIP) C8E.5: 5 residues within 4Å: Chain A: Y.91, Y.150, D.175 Chain C: H.21, F.23 4 PLIP interactions: 1 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:H.21, A:Y.91, A:Y.91, A:Y.150 C8E.6: 5 residues within 4Å: Chain A: V.298, G.299, Y.314, V.336 Chain D: F.85 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:Y.314, A:Y.314, D:F.85 C8E.7: 5 residues within 4Å: Chain B: V.298, G.299, V.312, Y.314 Chain F: F.85 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain F Hydrophobic interactions: B:V.298, B:V.312, B:Y.314, F:F.85 C8E.8: 4 residues within 4Å: Chain B: E.217, Y.219, Y.236, Y.240 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:Y.219, B:Y.219, B:Y.236 Hydrogen bonds: B:Y.219 C8E.9: 6 residues within 4Å: Chain B: Y.263, F.265 Chain F: P.78, Y.79, M.82 Ligands: LMT.22 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:Y.79 C8E.10: 5 residues within 4Å: Chain B: I.230, A.261, Q.262, Y.263, V.273 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.263 Hydrogen bonds: B:V.273 C8E.13: 6 residues within 4Å: Chain C: V.298, G.299, A.300, Y.314 Chain E: F.85 Ligands: C8E.20 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:A.300, C:Y.314 C8E.14: 8 residues within 4Å: Chain C: Y.263, F.265, D.266 Chain E: Y.79, K.80, M.82, Q.109 Ligands: C8E.15 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.265 C8E.15: 3 residues within 4Å: Chain C: A.261, Y.263 Ligands: C8E.14 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.263 Hydrogen bonds: C:Y.263 C8E.16: 8 residues within 4Å: Chain B: H.21, F.23, L.338, G.339, L.340 Chain C: Y.91, Y.150, D.175 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:L.338, B:L.340, C:Y.91 C8E.17: 2 residues within 4Å: Chain D: D.77 Ligands: C8E.1 No protein-ligand interaction detected (PLIP) C8E.18: 4 residues within 4Å: Chain D: F.73, L.74, G.76, Y.125 No protein-ligand interaction detected (PLIP) C8E.19: 5 residues within 4Å: Chain A: A.86, F.138 Chain E: P.51, N.54, L.99 4 PLIP interactions: 2 interactions with chain A, 2 interactions with chain E Hydrophobic interactions: A:A.86, A:F.138, E:N.54, E:L.99 C8E.20: 5 residues within 4Å: Chain C: F.23, D.25, V.312 Chain E: F.89 Ligands: C8E.13 3 PLIP interactions: 2 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:V.312, E:F.89 Hydrogen bonds: C:D.25 C8E.21: 3 residues within 4Å: Chain C: D.85, A.86, F.138 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:A.86

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

LMT.11: 9 residues within 4Å: Chain B: V.259, V.273, A.274, Y.275, K.294, V.296, L.318, D.320 Ligands: LMT.12 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.259, B:V.273, B:Y.275, B:Y.275, B:V.296 Hydrogen bonds: B:L.318, B:L.319 Salt bridges: B:K.294 LMT.12: 5 residues within 4Å: Chain B: Y.275, Q.277, K.279, K.294 Ligands: LMT.11 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:Q.277, B:Q.277, B:K.279, B:K.294, B:K.294 Salt bridges: B:K.279 LMT.22: 5 residues within 4Å: Chain F: G.76, D.77, P.78, K.80 Ligands: C8E.9 4 PLIP interactions: 4 interactions with chain F Hydrogen bonds: F:D.77, F:D.77, F:D.77, F:Y.79

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

OmpK36: ABC
ABC transporter permease: DEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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OmpK36

ABC transporter permease

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