6MJP

LptB(E163Q)FGC from Vibrio cholerae


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.242 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural basis of unidirectional export of lipopolysaccharide to the cell surface.

Owens, T.W.Taylor, R.J.Pahil, K.S.Bertani, B.R.Ruiz, N.Kruse, A.C.Kahne, D.

(2019) Nature 567: 550-553


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
ABC transporter ATP-binding protein
A, B
241Vibrio choleraeMutation(s): 1 
Gene Names: lptB
EC: 3.6.3.-
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Lipopolysaccharide transporter complex LptB2FGC
Find proteins for O30650 (Vibrio cholerae)
Go to UniProtKB:  O30650
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Lipopolysaccharide export system protein LptC
C
191Vibrio choleraeMutation(s): 0 
Gene Names: lptC
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Lipopolysaccharide transporter complex LptB2FGC
Find proteins for A0A085S5D1 (Vibrio cholerae)
Go to UniProtKB:  A0A085S5D1
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FIG000988: Predicted permease
F
366Vibrio choleraeMutation(s): 0 
Gene Names: lptF
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Lipopolysaccharide transporter complex LptB2FGC
Find proteins for A0A0F0BAF3 (Vibrio cholerae)
Go to UniProtKB:  A0A0F0BAF3
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
LPS export ABC transporter permease LptG
G
356Vibrio choleraeMutation(s): 0 
Gene Names: lptG
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
ATP Binding Cassette (ABC) Transporters
Protein: 
Lipopolysaccharide transporter complex LptB2FGC
Find proteins for A0A0H6JG76 (Vibrio cholerae)
Go to UniProtKB:  A0A0H6JG76
Small Molecules
Ligands 9 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JU7
Query on JU7

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F
6-cyclohexylhexyl beta-D-glucopyranoside
C18 H34 O6
IKXDBGTYPHAFNV-UYTYNIKBSA-N
 Ligand Interaction
CL
Query on CL

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Download CCD File 
A, B
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
GOL
Query on GOL

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B, G
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
CA
Query on CA

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A
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
PG4
Query on PG4

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A, B
TETRAETHYLENE GLYCOL
C8 H18 O5
UWHCKJMYHZGTIT-UHFFFAOYSA-N
 Ligand Interaction
MA4
Query on MA4

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G
CYCLOHEXYL-HEXYL-BETA-D-MALTOSIDE
C24 H44 O11
WUCWJXGMSXTDAV-QKMCSOCLSA-N
 Ligand Interaction
AE3
Query on AE3

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A
2-(2-ETHOXYETHOXY)ETHANOL
C6 H14 O3
XXJWXESWEXIICW-UHFFFAOYSA-N
 Ligand Interaction
LMT
Query on LMT

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Download CCD File 
F, G
DODECYL-BETA-D-MALTOSIDE
C24 H46 O11
NLEBIOOXCVAHBD-QKMCSOCLSA-N
 Ligand Interaction
PEG
Query on PEG

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Download CCD File 
B
DI(HYDROXYETHYL)ETHER
C4 H10 O3
MTHSVFCYNBDYFN-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.85 Å
  • R-Value Free: 0.292 
  • R-Value Work: 0.242 
  • Space Group: C 1 2 1
Unit Cell:
Length (Å)Angle (°)
a = 167.354α = 90.00
b = 80.729β = 112.18
c = 202.992γ = 90.00
Software Package:
Software NamePurpose
PHENIXrefinement
Aimlessdata scaling
XDSdata reduction
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01 GM066174
National Institutes of Health/National Institute Of Allergy and Infectious DiseasesUnited StatesR01 AI081059

Revision History 

  • Version 1.0: 2019-03-27
    Type: Initial release
  • Version 1.1: 2019-04-03
    Type: Data collection, Database references
  • Version 1.2: 2019-04-10
    Type: Data collection, Database references