3IJ9

Directed 'in situ' Elongation as a Strategy to Characterize the Covalent Glycosyl-Enzyme Catalytic Intermediate of Human Pancreatic a-Amylase

Structural Biology Knowledgebase: 3IJ9 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.184

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3IJ9

Classification: HYDROLASE

Total Structure Weight: 56752.00

Macromolecule Entities
Molecule Chains Length Organism Details
Pancreatic alpha-amylase A 496 Homo sapiens EC#: 3.2.1.1 IUBMB
Fragment: human pancreatic alpha-amylase
Mutation: Q1X
Gene Name(s): AMY2A Gene View

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
B0D
Query on B0D

A (2R,3S,4R,5R,6R)-2,6-difluoro-2-(hydroxymethyl)tetrahydro- 2H-pyran-3,4,5-triol
C6 H10 F2 O5
MGHYRMVVRYCAON-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
B9D
Query on B9D

A (2R,3R,4R,5S,6R)-6-fluoranyl-6-(hydroxymethyl)oxane- 2,3,4,5-tetrol
C6 H11 F O6
YQZCKDSOGGIGPL-DVKNGEFBSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
BGC
Query on BGC

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

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

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 1 Unique
ID Chains Type Formula 2D Diagram Parent
PCA
Query on PCA
A L-PEPTIDE LINKING C5 H7 N O3 GLU

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.85 Å
  • R-Value Free: 0.207
  • R-Value Work: 0.184
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 52.38 α = 90.00
b = 68.00 β = 90.00
c = 129.95 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2009-08-04
  • Released Date: 2009-10-27
  • Deposition author(s): Li, C., Zhang, R., Withers, S.G, Brayer, G.D.

Revision History

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