1J8V

Crystal structure of barley beta-D-glucan glucohydrolase isoenzyme Exo1 in complex with 4'-nitrophenyl 3I-thiolaminaritrioside

Structural Biology Knowledgebase: 1J8V SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.201

Literature

Macromolecules
Sequence Display for 1J8V

Classification: HYDROLASE

Total Structure Weight: 68226.84

Macromolecule Entities
Molecule Chains Length Organism Details
Beta-D-glucan glucohydrolase isoenzyme EXO1 A 605 Hordeum vulgare EC#: 3.2.1.58 IUBMB
Mutation: N320K
Gene Name(s):
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
LAM
Query on LAM

A 4'-NITROPHENYL-S-(BETA-D-GLUCOPYRANOSYL)- (1-3)-(3-THIO-BETA-D-GLUCOPYRANOSYL)-(1-3)- BETA-D-GLUCOPYRANOSIDE
4'-NITROPHENYL-3I-THIOLAMINARITRIOSIDE (Synonym)
C24 H35 N O17 S
VWNONHZCCMYIGR-VGNFVTAUSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BMA
Query on BMA

A BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAN
Query on MAN

A ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
FUC
Query on FUC

A ALPHA-L-FUCOSE
C6 H12 O5
SHZGCJCMOBCMKK-SXUWKVJYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
LAM N/A in BindingDB
Ki: 243200 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.250
  • R-Value Work: 0.201
  • Space Group: P 43 21 2

Unit Cell:

Length (Å) Angle (°)
a = 100.53 α = 90.00
b = 100.53 β = 90.00
c = 181.96 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-05-22
  • Released Date: 2002-06-12
  • Deposition author(s): Hrmova, M., De Gori, R., Smith, B.J., Fairweather, J.K., Driguez, H., Varghese, J.N., Fincher, G.B.

Revision History

  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4