1P6W

Crystal structure of barley alpha-amylase isozyme 1 (AMY1) in complex with the substrate analogue, methyl 4I,4II,4III-tri-thiomaltotetraoside (thio-DP4)

Structural Biology Knowledgebase: 1P6W SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.170

Literature

Macromolecules
Sequence Display for 1P6W

Classification: HYDROLASE

Total Structure Weight: 46336.41

Macromolecule Entities
Molecule Chains Length Organism Details
PROTEIN (Alpha-amylase type A isozyme) A 405 Hordeum vulgare EC#: 3.2.1.1 IUBMB
Mutation: A284V
Gene Name(s): AMY1.1
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A O1-METHYL-4-DEOXY-4-THIO-BETA-D-GLUCOSE
C7 H14 O5 S
PFROTWRHYMLGHR-NYMZXIIRSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
SGC
Query on SGC

A 4-DEOXY-4-THIO-BETA-D-GLUCOPYRANOSE
C6 H12 O5 S
KGSURTOFVLAWDC-QZABAPFNSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GLC
Query on GLC

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

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

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

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.216
  • R-Value Work: 0.170
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 93.43 α = 90.00
b = 72.10 β = 90.00
c = 60.88 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2003-04-30
  • Released Date: 2003-10-14
  • Deposition author(s): Robert, X., Haser, R., Aghajari, N.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4