1K1Y

Crystal structure of thermococcus litoralis 4-alpha-glucanotransferase complexed with acarbose

Structural Biology Knowledgebase: 1K1Y SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.198

Literature

Macromolecules
Sequence Display for 1K1Y

Classification: TRANSFERASE

Total Structure Weight: 157209.88

Macromolecule Entities
Molecule Chains Length Organism Details
4-ALPHA-GLUCANOTRANSFERASE A, B 659 Thermococcus litoralis EC#: 2.4.1.25 IUBMB
Gene Name(s): jgt OCC_10078
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

A ALPHA-ACARBOSE
1,4-DEOXY-4-((5-HYDROXYMETHYL-2,3,4-TRIHYDROXYCYCLOHEX- 5,6-ENYL)AMINO)FRUCTOSE (Synonym)
C25 H43 N O18
XUFXOAAUWZOOIT-WVJZLWNXSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MAL
Query on MAL

B MALTOSE
C12 H22 O11
GUBGYTABKSRVRQ-ASMJPISFSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
TRS
Query on TRS

B 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER (Synonym)
C4 H12 N O3
LENZDBCJOHFCAS-UHFFFAOYSA-O
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, B CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
ACR N/A in BindingDB
Ki: 600000 nM  BindingMOAD
Ki: 600000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.4 Å
  • R-Value Free: 0.256
  • R-Value Work: 0.198
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 137.61 α = 90.00
b = 160.97 β = 90.00
c = 70.20 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2001-09-26
  • Released Date: 2003-06-17
  • Deposition author(s): Imamura, H., Fushinobu, S., Kumasaka, T., Yamamoto, M., Jeon, B.S., Wakagi, T., Matsuzawa, H.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values