4M1U

The crystal structure of Stx2 and a disaccharide ligand

Structural Biology Knowledgebase: 4M1U SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.170

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4M1U

Classification: HYDROLASE

Total Structure Weight: 73750.24

Macromolecule Entities
Molecule Chains Length Organism Details
Shiga toxin 2 A-subunit A 297 Escherichia coli EC#: 3.2.2.22 IUBMB
Fragment: Stx2 subunit A (unp entries 230-319)
Gene Name(s): stx2 A-subunit stx 2 A-subunit stx2A ECs1205 Z1464 AO055_12930 ASO15_06230
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Shiga toxin 2 B subunit B, C, D, E, F 70 Escherichia coli Fragment: Stx2 subunit B (unp entries 20-89)
Gene Name(s): stxII stx2B stx2dB stx2vB stxB2 vtx2B AGA26_00045 HW42_08855 UN91_26180 WQ91_20000 WR04_15075 WR13_20980 WR17_25095
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
A2G
Query on A2G

F N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
C8 H15 N O6
OVRNDRQMDRJTHS-CBQIKETKSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
1PS
Query on 1PS

B, C, D 3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
PPS, (Synonym)
C8 H11 N O3 S
REEBJQTUIJTGAL-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MBG
Query on MBG

F METHYL-BETA-GALACTOSE
C7 H14 O6
HOVAGTYPODGVJG-VOQCIKJUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.56 Å
  • R-Value Free: 0.192
  • R-Value Work: 0.170
  • Space Group: P 61
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 146.25 α = 90.00
b = 146.25 β = 90.00
c = 60.31 γ = 120.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2013-08-04
  • Released Date: 2013-11-20
  • Deposition author(s): Yin, J., James, M.N.G., Jacobson, J.M., Kitov, P.I., Bundle, D.R., Mulvey, G., Armstrong, G.

Revision History

  • 2014-02-19
    Type: Citation | Details: Citation update
  • 2013-12-04
    Type: Citation | Details: Citation update