SMTL ID : 6mjp.1

LptB(E163Q)FGC from Vibrio cholerae

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.85 Å

Oligo State

hetero-2-1-1-1-mer

Ligands

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.1: 5 residues within 4Å: Chain A: G.39, G.41, K.42, T.43, T.44 Ligand excluded by PLIP CL.2: 1 residues within 4Å: Chain A: I.179 Ligand excluded by PLIP CL.5: 2 residues within 4Å: Chain A: V.197, R.198 Ligand excluded by PLIP CL.9: 6 residues within 4Å: Chain B: G.39, A.40, G.41, K.42, T.43, T.44 Ligand excluded by PLIP

2 x CA: CALCIUM ION(Non-covalent)

CA.3: 2 residues within 4Å: Chain A: E.112, D.116 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.112, A:D.116, A:D.116, H2O.1 CA.4: 2 residues within 4Å: Chain A: N.196 Chain B: N.196 No protein-ligand interaction detected (PLIP)

2 x AE3: 2-(2-ETHOXYETHOXY)ETHANOL(Non-covalent)

AE3.6: 4 residues within 4Å: Chain A: A.2, I.3, S.28, D.63 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:A.2, A:D.63 AE3.7: 4 residues within 4Å: Chain A: N.155, P.156, Q.157, R.186 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:N.155, A:Q.157

2 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.8: 6 residues within 4Å: Chain A: Y.47, L.52, E.86 Chain E: A.82, S.85, V.88 No protein-ligand interaction detected (PLIP) PG4.10: 6 residues within 4Å: Chain A: G.141, R.144, G.167, I.176, I.179 Chain B: N.38 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.38

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.11: 4 residues within 4Å: Chain B: Y.82, P.84, Q.85, E.86 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.85, B:E.86, B:D.162

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.12: 2 residues within 4Å: Chain B: I.3, D.63 No protein-ligand interaction detected (PLIP) GOL.13: 2 residues within 4Å: Chain B: G.51, L.52 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.51 GOL.19: 1 residues within 4Å: Chain E: D.99 2 PLIP interactions: 2 interactions with chain E Hydrogen bonds: E:D.99 Water bridges: E:S.96

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

LMT.14: 9 residues within 4Å: Chain C: S.4, Y.8, L.11 Chain D: L.286, I.305, L.338, A.341, V.345, L.348 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:I.305, D:L.338, D:V.345 LMT.16: 13 residues within 4Å: Chain C: R.5 Chain D: F.296, A.297, M.299, G.300, P.301, I.303 Chain E: M.301, G.302, I.305, L.306, V.309 Ligands: LMT.18 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: E:V.309 Hydrogen bonds: E:G.302, C:R.5, D:G.300 LMT.18: 15 residues within 4Å: Chain A: R.91, K.92 Chain E: Y.8, R.11, T.12, T.16, L.19, L.72, I.76, A.80, S.84, E.86, M.301, I.305 Ligands: LMT.16 9 PLIP interactions: 8 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:L.72, E:I.76, E:I.305 Hydrogen bonds: E:Y.8, E:R.11, E:T.16, E:A.80, E:S.84 Salt bridges: A:K.92

1 x JU7: 6-cyclohexylhexyl beta-D-glucopyranoside(Non-covalent)

JU7.15: 8 residues within 4Å: Chain B: R.91, K.92 Chain D: E.10, R.78, E.82, R.295, F.296 Ligands: MA4.17 5 PLIP interactions: 4 interactions with chain D, 1 interactions with chain B Hydrophobic interactions: D:F.296 Hydrogen bonds: D:E.82, B:R.91 Salt bridges: D:R.78, D:R.295

1 x MA4: CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE(Non-covalent)

MA4.17: 8 residues within 4Å: Chain D: E.82, R.295 Chain E: L.296, S.298, V.299, A.303, S.307 Ligands: JU7.15 4 PLIP interactions: 3 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:L.296, E:V.299 Hydrogen bonds: E:S.298 Salt bridges: D:R.295

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Owens, T.W. et al., Structural basis of unidirectional export of lipopolysaccharide to the cell surface. Nature (2019)

Release Date

2019-03-27

Peptides

ABC transporter ATP-binding protein: AB
Lipopolysaccharide export system protein LptC: C
FIG000988: Predicted permease: D
LPS export ABC transporter permease LptG: E

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
F

E
G

Membrane

We predict this structure to be a membrane protein.
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ABC transporter ATP-binding protein

Lipopolysaccharide export system protein LptC

FIG000988: Predicted permease

LPS export ABC transporter permease LptG