1DOG

REFINED STRUCTURE FOR THE COMPLEX OF 1-DEOXYNOJIRIMYCIN WITH GLUCOAMYLASE FROM (ASPERGILLUS AWAMORI) VAR. X100 TO 2.4 ANGSTROMS RESOLUTION

Structural Biology Knowledgebase: 1DOG SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Observed: 0.119

Literature

Macromolecules
Sequence Display for 1DOG

Classification: HYDROLASE

Total Structure Weight: 54887.30

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
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)
NOJ
Query on NOJ

A 1-DEOXYNOJIRIMYCIN
MORANOLINE (Synonym)
C6 H13 N O4
LXBIFEVIBLOUGU-JGWLITMVSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
NOJ N/A in BindingDB
Ki: 96000 nM  BindingMOAD
N/A in PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.3 Å
  • R-Value Observed: 0.119
  • Space Group: P 21 21 21

Unit Cell:

Length (Å) Angle (°)
a = 116.60 α = 90.00
b = 103.60 β = 90.00
c = 48.30 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1993-01-12
  • Released Date: 1994-01-31
  • Deposition author(s): Harris, E., Aleshin, A., Firsov, L., Honzatko, R.B.

Revision History

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