5YSD

Crystal structure of beta-1,2-glucooligosaccharide binding protein in complex with sophorotriose


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural and thermodynamic insights into beta-1,2-glucooligosaccharide capture by a solute-binding protein inListeria innocua.

Abe, K.Sunagawa, N.Terada, T.Takahashi, Y.Arakawa, T.Igarashi, K.Samejima, M.Nakai, H.Taguchi, H.Nakajima, M.Fushinobu, S.

(2018) J. Biol. Chem. 293: 8812-8828


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Lin1841 protein
A, B
397Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262)Mutation(s): 0 
Find proteins for Q92AS8 (Listeria innocua serovar 6a (strain ATCC BAA-680 / CLIP 11262))
Go to UniProtKB:  Q92AS8
Small Molecules
Ligands 4 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
BGC
Query on BGC

Download SDF File 
Download CCD File 
A, B
BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
 Ligand Interaction
GLC
Query on GLC

Download SDF File 
Download CCD File 
A, B
ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
A
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
MPD
Query on MPD

Download SDF File 
Download CCD File 
A, B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.207 
  • R-Value Work: 0.169 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 36.082α = 90.00
b = 125.561β = 101.61
c = 91.780γ = 90.00
Software Package:
Software NamePurpose
HKL-2000data processing
MOLREPphasing
REFMACrefinement
Cootrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2018-05-02
    Type: Initial release
  • Version 1.1: 2018-06-20
    Type: Data collection, Database references