2BEH

Crystal structure of antithrombin variant S137A/V317C/T401C with plasma latent antithrombin

Structural Biology Knowledgebase: 2BEH SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.219

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2BEH

Classification: BLOOD CLOTTING

Total Structure Weight: 100162.98

Macromolecule Entities
Molecule Chains Length Organism Details
Antithrombin-III I 432 Homo sapiens Mutation: S137A, V317C, T401C
Gene Name(s): SERPINC1 Gene View AT3 PRO0309
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Antithrombin-III L 432 Homo sapiens Gene Name(s): SERPINC1 Gene View AT3 PRO0309

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

I, L N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NDG
Query on NDG

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

I ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
GOL
Query on GOL

I GLYCEROL
2, (Synonym)
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.265
  • R-Value Work: 0.219
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 68.07 α = 90.00
b = 97.27 β = 105.03
c = 87.39 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2005-10-24
  • Released Date: 2005-11-01
  • Deposition author(s): Johnson, D.J., Luis, S.A., Huntington, J.A.

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