2F2H

Structure of the YicI thiosugar Michaelis complex

Structural Biology Knowledgebase: 2F2H SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.180

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2F2H

Classification: HYDROLASE

Total Structure Weight: 536218.14

Macromolecule Entities
Molecule Chains Length Organism Details
Putative family 31 glucosidase yicI A, B, C..., D, E, FA, B, C, D, E, F 773 Escherichia coli EC#: 3.2.1.177 IUBMB
Gene Name(s): yicI b3656 JW3631

Small Molecules
Ligands 4 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
XTG
Query on XTG

A, B, C, D, E, F 4-NITROPHENYL 6-THIO-6-S-ALPHA-D-XYLOPYRANOSYL- BETA-D-GLUCOPYRANOSIDE
4-NITROPHENYL-(6-S-ALPHA-D-XYLOPYRANOSYL)- BETA-D-GLUCOPYRANOSIDE (Synonym)
C17 H23 N O11 S
HQYVHBCTLFPWRQ-ZMFOIVQCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MPO
Query on MPO

B, C, D, E, F 3[N-MORPHOLINO]PROPANE SULFONIC ACID
C7 H15 N O4 S
DVLFYONBTKHTER-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SO4
Query on SO4

A, B, C, D, E, F SULFATE ION
O4 S
QAOWNCQODCNURD-UHFFFAOYSA-L
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

A, B, C, D, E, F GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
XTG N/A in BindingDB
Ki: 2000 nM  BindingMOAD
Ki: 2000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.95 Å
  • R-Value Free: 0.225
  • R-Value Work: 0.180
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 162.32 α = 90.00
b = 175.84 β = 90.00
c = 210.74 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-11-16
  • Released Date: 2006-02-28
  • Deposition author(s): Kim, Y.-W., Lovering, A.L., Strynadka, N.C.J., Withers, S.G.

Revision History

  • 2011-07-13
    Type: Flag residual B-value | Details: Tagged residual B temperature factor
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4