1M1J

Crystal structure of native chicken fibrinogen with two different bound ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Crystal Structure of Native Chicken Fibrinogen at 2.7 A Resolution

Yang, Z.Kollman, J.M.Pandi, L.Doolittle, R.F.

(2001) Biochemistry 40: 12515-12523


  • PubMed Abstract: 
  • The crystal structure of native chicken fibrinogen (320 kDa) complexed with two synthetic peptides has been determined at a resolution of 2.7 A. The structure provides the first atomic-resolution view of the polypeptide chain arrangement in the centr ...

    The crystal structure of native chicken fibrinogen (320 kDa) complexed with two synthetic peptides has been determined at a resolution of 2.7 A. The structure provides the first atomic-resolution view of the polypeptide chain arrangement in the central domain where the two halves of the molecule are joined, as well as of a putative thrombin-binding site. The amino-terminal segments of the alpha and beta chains, including fibrinopeptides A and B, are not visible in electron density maps, however, and must be highly disordered. The alphaC domain is also very disordered. A residue by residue analysis of the coiled coils with regard to temperature factor shows a strong correlation between mobility and plasmin attack sites. It is concluded that structural flexibility is an inherent feature of fibrinogen that plays a key role in both its conversion to fibrin and its subsequent destruction by plasmin.


    Related Citations: 
    • Crystal Structure of Native Chicken Fibrinogen at 5.5-A Resolution
      Yang, Z.,Mochalkin, I.,Veerapandian, L.,Riley, M.,Doolittle, R.F.
      (2000) Proc.Natl.Acad.Sci.USA 97: 3907
    • Crystal Structure of Fragment Double-d from Human Fibrin with Two Different Bound Ligands
      Everse, S.J.,Spraggon, G.,Veerapandian, L.,Riley, M.,Doolittle, R.F.
      (1998) Biochemistry 37: 8637
    • Crystal Sturctures of Fragment D from Human Fibrinogen and its Crosslinked Counterpart from Fibrin
      Spraggon, G.,Everse, S.J.,Doolittle, R.F.
      (1997) Nature 389: 455


    Organizational Affiliation

    Center for Molecular Genetics, University of California, San Diego, La Jolla, California 92093-0634, USA.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen alpha subunit
A, D
491Gallus gallusGene Names: FGA
Find proteins for P14448 (Gallus gallus)
Go to Gene View: FGA
Go to UniProtKB:  P14448
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen beta chain
B, E
464Gallus gallusGene Names: FGB
Find proteins for Q02020 (Gallus gallus)
Go to Gene View: FGB
Go to UniProtKB:  Q02020
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen gamma chain
C, F
409Gallus gallusN/A
Find proteins for O93568 (Gallus gallus)
Go to UniProtKB:  O93568
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
GLY-PRO-ARG-PRO peptide
G, H
4N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
GLY-HIS-ARG-PRO peptide
I, J
4N/AN/A
Protein Feature View is not available: No corresponding UniProt sequence found.
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
B, C, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NDG
Query on NDG

Download SDF File 
Download CCD File 
B, C, E, F, J
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download SDF File 
Download CCD File 
C, F, I
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.7 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 114.090α = 90.00
b = 100.020β = 105.79
c = 200.090γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
DENZOdata reduction
CNSrefinement
AMoREphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-26
    Type: Initial release
  • Version 1.1: 2008-04-28
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance