1M1J

Crystal structure of native chicken fibrinogen with two different bound ligands


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.227 

wwPDB Validation 3D Report Full Report



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

  • DOI: 10.1021/bi011394p
  • Structures With Same Primary Citation

  • 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 U S A 97: 3907
    • 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
    • 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

    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 subunitA, D491Gallus gallusMutation(s): 0 
Gene Names: FGA
Find proteins for P14448 (Gallus gallus)
Explore P14448 
Go to UniProtKB:  P14448
Protein Feature View
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  • Reference Sequence
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
GLY-HIS-ARG-PRO peptideI, J4N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence

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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen beta chainB, E464Gallus gallusMutation(s): 0 
Gene Names: FGB
Find proteins for Q02020 (Gallus gallus)
Explore Q02020 
Go to UniProtKB:  Q02020
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  • Reference Sequence

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
Fibrinogen gamma chainC, F409Gallus gallusMutation(s): 0 
Find proteins for O93568 (Gallus gallus)
Explore O93568 
Go to UniProtKB:  O93568
Protein Feature View
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
GLY-PRO-ARG-PRO peptideG, H4N/AMutation(s): 0 
Protein Feature View
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download CCD File 
B, C, E, F, J
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
 Ligand Interaction
NAG
Query on NAG

Download CCD File 
C, F, I
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
CA
Query on CA

Download CCD File 
B, C, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.70 Å
  • R-Value Free: 0.256 
  • R-Value Work: 0.227 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 114.09α = 90
b = 100.02β = 105.79
c = 200.09γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
CNSrefinement

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2002-06-26
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary