2GVY

Monoclinic crystal form of Aspergillus niger alpha-amylase in complex with maltose at 1.8 A resolution

Structural Biology Knowledgebase: 2GVY SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.162

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2GVY

Classification: HYDROLASE

Total Structure Weight: 107629.58

Macromolecule Entities
Molecule Chains Length Organism Details
Alpha-amylase A A, B 478 Aspergillus oryzae EC#: 3.2.1.1 IUBMB
Gene Name(s): amy1 amyI Taa-G1 AO090023000944 amy2 amyII Taa-G2 AO090120000196

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

B 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

A, B ALPHA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-DVKNGEFBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BGC
Query on BGC

A, B BETA-D-GLUCOSE
C6 H12 O6
WQZGKKKJIJFFOK-VFUOTHLCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.210
  • R-Value Work: 0.162
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 65.45 α = 90.00
b = 101.15 β = 103.89
c = 75.18 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-05-03
  • Released Date: 2006-08-15
  • Deposition author(s): Vujicic-Zagar, A., Dijkstra, B.W.

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