SMTL ID : 5nur.1

Structural basis for maintenance of bacterial outer membrane lipid asymmetry

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 3.29 Å

Oligo State

hetero-3-3-mer

Ligands

1 x GP1- Z9M- KDO- KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose

GP1-Z9M-KDO-KDO.1: 9 residues within 4Å: Chain A: N.207, G.208, K.209, K.210, E.212, R.235, N.236, N.252 Ligands: CA.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:K.210, A:K.210, A:K.209, A:K.210, A:K.210, A:N.236, A:N.236, A:E.212, A:R.235 Salt bridges: A:R.235, A:K.253

1 x GP1- Z9M- KDO- KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-4)-3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(2-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose

GP1-Z9M-KDO-KDO.2: 9 residues within 4Å: Chain C: N.207, G.208, E.212, R.235, N.236, N.252, K.253, D.282 Ligands: CA.10 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:E.212, C:E.212, C:N.207, C:N.207, C:N.236, C:D.282, C:E.212 Salt bridges: C:R.235, C:K.253

1 x GP1- Z9M- KDO: 3-deoxy-alpha-D-manno-oct-2-ulopyranosonic acid-(3-6)-2-amino-2-deoxy-4-O-phosphono-beta-D-glucopyranose-(1-6)-2-amino-2-deoxy-1-O-phosphono-alpha-D-glucopyranose

GP1-Z9M-KDO.3: 6 residues within 4Å: Chain E: K.210, E.212, R.235, N.252, K.253 Ligands: CA.14 4 PLIP interactions: 4 interactions with chain E Hydrogen bonds: E:K.210, E:K.210, E:N.252, E:E.212, E:R.235 Salt bridges: E:R.235, E:K.253

3 x CA: CALCIUM ION(Non-covalent)

CA.4: 4 residues within 4Å: Chain A: N.207, N.236, N.252 Ligands: GP1-Z9M-KDO-KDO.1 1 PLIP interactions: 1 interactions with chain A Metal complexes: A:N.207 CA.10: 4 residues within 4Å: Chain C: N.207, N.236, N.252 Ligands: GP1-Z9M-KDO-KDO.2 1 PLIP interactions: 1 interactions with chain C Metal complexes: C:N.207 CA.14: 4 residues within 4Å: Chain E: N.207, N.236, N.252 Ligands: GP1-Z9M-KDO.3 1 PLIP interactions: 1 interactions with chain E Metal complexes: E:N.207

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

SO4.5: 3 residues within 4Å: Chain A: R.42, R.82, R.132 3 PLIP interactions: 3 interactions with chain A Salt bridges: A:R.42, A:R.82, A:R.132 SO4.6: 3 residues within 4Å: Chain A: S.125, R.167, R.168 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.167, A:R.168 SO4.7: 5 residues within 4Å: Chain A: T.165, R.167, R.168 Chain E: G.72, A.73 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain E Hydrogen bonds: A:T.165, E:A.73 Salt bridges: A:R.168 SO4.11: 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 SO4.12: 5 residues within 4Å: Chain A: G.72, A.73 Chain C: T.165, R.167, R.168 4 PLIP interactions: 1 interactions with chain A, 3 interactions with chain C Hydrogen bonds: A:A.73, C:T.165, C:T.165 Salt bridges: C:R.168 SO4.15: 3 residues within 4Å: Chain E: R.42, R.82, R.132 3 PLIP interactions: 3 interactions with chain E Salt bridges: E:R.42, E:R.82, E:R.132 SO4.16: 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 SO4.17: 3 residues within 4Å: Chain E: S.125, R.167, R.168 3 PLIP interactions: 3 interactions with chain E Hydrogen bonds: E:S.125 Salt bridges: E:R.167, E:R.168

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

C8E.8: 7 residues within 4Å: Chain A: H.21, F.23, G.26, V.334 Chain C: Y.98, Y.157, D.172 7 PLIP interactions: 4 interactions with chain C, 3 interactions with chain A Hydrophobic interactions: C:Y.98, C:Y.98, C:Y.157, A:F.23, A:F.23, A:V.334 Hydrogen bonds: C:Y.157 C8E.9: 10 residues within 4Å: Chain B: P.51, N.54, G.55, N.58, M.96, L.99, I.100 Chain C: V.93, Y.139, F.145 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:N.54 Hydrogen bonds: B:N.58 C8E.13: 9 residues within 4Å: Chain C: H.21, F.23, K.25, G.26, V.334 Chain E: Y.98, Y.157, G.159, D.172 7 PLIP interactions: 4 interactions with chain E, 3 interactions with chain C Hydrophobic interactions: E:Y.98, E:Y.98, E:Y.98, E:Y.157, C:F.23, C:V.334 Hydrogen bonds: C:G.26

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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