1XD0

Acarbose Rearrangement Mechanism Implied by the Kinetic and Structural Analysis of Human Pancreatic alpha-Amylase in Complex with Analogues and Their Elongated Counterparts

Structural Biology Knowledgebase: 1XD0 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.175

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 1XD0

Classification: HYDROLASE

Total Structure Weight: 57036.39

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

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

A ACARBOSE DERIVED PENTASACCHARIDE
4-O-(4,6-DIDEOXY-4-{[4-[(4-O-HEXOPYRANOSYLHEXOPYRANOSYL)OXY]- 5,6-DIHYDROXY-3-(HYDROXYMETHYL)CYCLOHEX-2- EN-1-YL]AMINO}HEXOPYRANOSYL)HEXOPYRANOSE (Synonym)
C31 H53 N O23
JUCZMZWYUIRMPL-NPPSNIQKSA-N
Ligand Explorer
 
JSmol
CA
Query on CA

A CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
JSmol
CL
Query on CL

A CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Ligand Explorer
 
JSmol
NAG
Query on NAG

A N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
JSmol
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ARE N/A in BindingDB
Ki: 75 nM  BindingMOAD
Ki: 75 nM  PDBbind
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: 2.0 Å
  • R-Value Free: 0.199
  • R-Value Work: 0.175
  • Space Group: P 21 21 21
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 52.90 α = 90.00
b = 68.90 β = 90.00
c = 132.00 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2004-09-03
  • Released Date: 2004-12-07
  • Deposition author(s): Li, C., Begum, A., Numao, S., Park, K.H., Withers, S.G., Brayer, G.D.

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