2GD4

Crystal Structure of the Antithrombin-S195A Factor Xa-Pentasaccharide Complex

Structural Biology Knowledgebase: 2GD4 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.298
  • R-Value Work: 0.247

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 2GD4

Classification: HYDROLASE

Total Structure Weight: 173131.77

Macromolecule Entities
Molecule Chains Length Organism Details
Coagulation factor X, Stuart factor, Stuart-Prower factor, Contains: Factor X light chain; Factor X heavy chain; Activated factor Xa heavy chain A, L 58 Homo sapiens EC#: 3.4.21.6 IUBMB
Fragment: Residues 126-182
Gene Name(s): F10 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Coagulation factor, Stuart factor, Stuart-Prower factor, Contains: Factor X light chain; Factor X heavy chain; Activated factor Xa heavy chain B, H 241 Homo sapiens EC#: 3.4.21.6 IUBMB
Fragment: Residues 235-475
Mutation: S104A
Gene Name(s): F10 Gene View
Antithrombin-III C, I 443 Homo sapiens Fragment: Residues 22-464
Mutation: S137A, E347A, K348A, K350A
Gene Name(s): SERPINC1 Gene View AT3 PRO0309
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

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

C, I TRISULFOAMINO HEPARIN PENTASACCHARIDE
C31 H53 N3 O49 S8
KANJSNBRCNMZMV-ABRZTLGGSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
NAG
Query on NAG

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

I BETA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-RWOPYEJCSA-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)
CA
Query on CA

B, H CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.298
  • R-Value Work: 0.247
  • Space Group: C 1 2 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 220.26 α = 90.00
b = 60.59 β = 113.14
c = 156.17 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2006-03-15
  • Released Date: 2006-05-09
  • Deposition author(s): Johnson, D.J., Li, W., Adams, T.E., Huntington, J.A.

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4
  • 2011-07-13
    Type: Non-polymer description | Details: chemical name/synonym update