1UJ3

Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal structure of a humanized Fab fragment of anti-tissue-factor antibody in complex with tissue factor.

Ohto, U.Mizutani, R.Nakamura, M.Adachi, H.Satow, Y.

(2004) J.Synchrotron Radiat. 11: 105-108


  • PubMed Abstract: 
  • Tissue factor (TF) is a membrane-anchored protein that initiates the extrinsic cascade of blood coagulation. TF forms a complex with serine protease Factor VIIa, and then activates Factor X zymogen to Factor Xa, leading to the blood coagulation. Huma ...

    Tissue factor (TF) is a membrane-anchored protein that initiates the extrinsic cascade of blood coagulation. TF forms a complex with serine protease Factor VIIa, and then activates Factor X zymogen to Factor Xa, leading to the blood coagulation. Humanized anti-TF antibody hATR-5 strongly inhibits TF-initiated blood coagulation, and is of potential use for various thrombotic diseases. The Fab fragment of antibody hATR-5 is obtained for crystallization. The crystal structure of the complex of the Fab with extracellular domains of human TF was determined with the molecular replacement method, and refined to an R factor of 0.196 at 2.1 A resolution. All the complementarity-determining regions (CDRs) of the Fab are involved in interaction with the C-terminal-side extracellular domain of TF through 19 hydrogen bonds. The interface between the Fab and TF molecules contains 15 water molecules, and yields buried surface areas as wide as 2000 A2. The TF surface in the interface is possibly involved in the activation of Factor X, by forming a transient ternary complex of Factor X-TF-Factor VIIa. Electrostatic interactions are predominantly observed between the heavy-chain CDRs and TF. These hydrogen-bonding and electrostatic interactions together with the wide buried areas contribute to the high affinity of the antibody toward TF, leading to the effective inhibition of the TF-initiated blood coagulation.


    Organizational Affiliation

    Graduate School of Pharmaceutical Sciences, University of Tokyo, 7-3-1 Hongo, Bunkyo, Tokyo 113-0033, Japan.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
IgG Fab light chain
A
215N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
IgG Fab heavy chain
B
217N/AMutation(s): 0 
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
tissue factor
C
205Homo sapiensMutation(s): 0 
Gene Names: F3
Find proteins for P13726 (Homo sapiens)
Go to Gene View: F3
Go to UniProtKB:  P13726
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.1 Å
  • R-Value Free: 0.227 
  • R-Value Work: 0.196 
  • Space Group: P 21 21 2
Unit Cell:
Length (Å)Angle (°)
a = 103.054α = 90.00
b = 265.996β = 90.00
c = 42.254γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
CNSphasing
CCP4data scaling

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2004-07-25
    Type: Initial release
  • Version 1.1: 2008-04-27
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Version format compliance