1DE7

INTERACTION OF FACTOR XIII ACTIVATION PEPTIDE WITH ALPHA-THROMBIN: CRYSTAL STRUCTURE OF THE ENZYME-SUBSTRATE COMPLEX

Structural Biology Knowledgebase: 1DE7 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.194

Literature

Macromolecules
Sequence Display for 1DE7

Classification: HYDROLASE / HYDROLASE SUBSTRATE

Total Structure Weight: 70065.52

Macromolecule Entities
Molecule Chains Length Organism Details
ALPHA-THROMBIN (LIGHT CHAIN) J, L 36 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
ALPHA-THROMBIN (HEAVY CHAIN) H, K 259 Homo sapiens EC#: 3.4.21.5 IUBMB
Gene Name(s): F2 Gene View
FACTOR XIII ACTIVATION PEPTIDE (28-37) A, B 11 synthetic

Small Molecules
Ligands 1 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
NA
Query on NA

H, K SODIUM ION
Na
FKNQFGJONOIPTF-UHFFFAOYSA-N
Ligand Explorer NGL
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
Modified Residues 2 Unique
ID Chains Type Formula 2D Diagram Parent
AR7
Query on AR7
A, B peptide-like C6 H17 N4 O2 ARG
0QE
Query on 0QE
A, B NON-POLYMER C H3 Cl --

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.0 Å
  • R-Value Free: 0.257
  • R-Value Work: 0.194
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 54.07 α = 90.00
b = 81.26 β = 101.62
c = 85.46 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 1999-11-13
  • Released Date: 2000-12-13
  • Deposition author(s): Sadasivan, C., Yee, V.C.

Revision History

  • 2011-07-13
    Type: Linkage | Details: Linkage
  • 2011-07-13
    Type: Sequence database correspondence | Details: Sequence database correspondence
  • 2011-07-13
    Type: Polymer description | Details: Changed inhibitor presentation or chemistry
  • 2011-07-13
    Type: Biological assembly | Details: Added software calculated values
  • 2011-07-13
    Type: Atom nomenclature | Details: Atom nomenclature
  • 2011-07-13
    Type: Binding sites and description | Details: Binding sites and description
  • 2011-07-13
    Type: Non-polymer description | Details: Non-polymer description
  • 2011-07-13
    Type: Function and keywords | Details: Function and keywords
  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4