6C9W

Crystal Structure of a ligand bound LacY/Nanobody Complex


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.276 

wwPDB Validation 3D Report Full Report


This is version 1.3 of the entry. See complete history

Literature

Crystal Structure of a ligand-bound LacY-Nanobody Complex.

Kumar, H.Finer-Moore, J.S.Jiang, X.Smirnova, I.Kasho, V.Pardon, E.Steyaert, J.Kaback, H.R.Stroud, R.M.

(2018) Proc. Natl. Acad. Sci. U.S.A. 115: 8769-8774


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lactose permease
A
417Escherichia coli (strain K12)Mutation(s): 2 
Gene Names: lacY
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
Major Facilitator Superfamily (MFS) Transporters
Protein: 
LacY Lactose Permease Transporter (C154G mutant)
Find proteins for P02920 (Escherichia coli (strain K12))
Go to UniProtKB:  P02920
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Nanobody9047
B
125N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
9PG
Query on 9PG

Download SDF File 
Download CCD File 
A
4-nitrophenyl alpha-D-galactopyranoside
C12 H15 N O8
IFBHRQDFSNCLOZ-IIRVCBMXSA-N
 Ligand Interaction
BNG
Query on BNG

Download SDF File 
Download CCD File 
A
B-NONYLGLUCOSIDE
C15 H30 O6
QFAPUKLCALRPLH-UXXRCYHCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3 Å
  • R-Value Free: 0.295 
  • R-Value Work: 0.276 
  • Space Group: P 65 2 2
Unit Cell:
Length (Å)Angle (°)
a = 153.550α = 90.00
b = 153.550β = 90.00
c = 193.680γ = 120.00
Software Package:
Software NamePurpose
PDB_EXTRACTdata extraction
XDSdata reduction
PHENIXrefinement
XSCALEdata scaling
PHENIXphasing

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 General Medical SciencesUnited StatesGM120043

Revision History 

  • Version 1.0: 2018-08-15
    Type: Initial release
  • Version 1.1: 2018-08-29
    Type: Data collection, Database references
  • Version 1.2: 2018-09-05
    Type: Data collection, Database references
  • Version 1.3: 2019-02-20
    Type: Author supporting evidence, Data collection