1AGM

Refined structure for the complex of acarbose with glucoamylase from Aspergillus awamori var. x100 to 2.4 angstroms resolution

Structural Biology Knowledgebase: 1AGM SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Observed: 0.124

Literature

Macromolecules
Sequence Display for 1AGM

Classification: HYDROLASE

Total Structure Weight: 55852.18

Macromolecule Entities
Molecule Chains Length Organism Details
GLUCOAMYLASE-471 A 470 Aspergillus awamori EC#: 3.2.1.3 IUBMB
Mutation: I58L, L60I, A117T
Gene Name(s): GLAA
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ALPHA-ACARBOSE
1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX- 5,6-ENYL)AMINO)FRUCTOSE (Synonym)
C25 H43 N O18
XUFXOAAUWZOOIT-WVJZLWNXSA-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)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ACR N/A in BindingDB
Kd: 0.001 nM  BindingMOAD
Ki: 0.001 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Observed: 0.124
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 116.70 α = 90.00
b = 103.90 β = 90.00
c = 48.34 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1994-05-13
  • Released Date: 1994-09-30
  • Deposition author(s): Aleshin, A.E., Firsov, L.M., Honzatko, R.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