1FZC

CRYSTAL STRUCTURE OF FRAGMENT DOUBLE-D FROM HUMAN FIBRIN WITH TWO DIFFERENT BOUND LIGANDS


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.220 

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Literature

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: 8637-8642

  • DOI: 10.1021/bi9804129
  • Primary Citation of Related Structures:  
    1FZC

  • PubMed Abstract: 
  • Factor XIII-cross-linked fragment D (double-D) from human fibrin was crystallized in the presence of two different peptide ligands and the X-ray structure determined at 2.3 A. The peptide Gly-Pro-Arg-Pro-amide, which is an analogue of the knob exposed by ...

    Factor XIII-cross-linked fragment D (double-D) from human fibrin was crystallized in the presence of two different peptide ligands and the X-ray structure determined at 2.3 A. The peptide Gly-Pro-Arg-Pro-amide, which is an analogue of the knob exposed by the thrombin-catalyzed removal of fibrinopeptide A, was found to reside in the gamma-chain holes, and the peptide Gly-His-Arg-Pro-amide, which corresponds to the beta-chain knob, was found in the homologous beta-chain holes. The structure shows for the first time that the beta-chain knob does indeed bind to a homologous hole on the beta-chain. The gamma- and beta-chain holes are structurally very similar, and it is remarkable they are able to distinguish between these two peptides that differ by a single amino acid. Additionally, we have found that the beta-chain domain, like its gamma-chain counterpart, binds calcium.


    Related Citations: 
    • Crystal Structures of Fragment D from Human Fibrinogen and its Crosslinked Counterpart from Fibrin
      Spraggon, G., Everse, S.J., Doolittle, R.F.
      (1997) Nature 389: 455
    • Erratum. Crystal Structures of Fragment D from Human Fibrinogen and its Crosslinked Counterpart from Fibrin
      Spraggon, G., Everse, S.J., Doolittle, R.F.
      (1997) Nature 390: 315

    Organizational Affiliation

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FIBRIN AD87Homo sapiensMutation(s): 0 
Gene Names: FGA
Find proteins for P02671 (Homo sapiens)
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PHAROS:  P02671
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FIBRIN BE328Homo sapiensMutation(s): 0 
Gene Names: FGB
Find proteins for P02675 (Homo sapiens)
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PHAROS:  P02675
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FIBRIN CF319Homo sapiensMutation(s): 0 
Gene Names: FGGPRO2061
Find proteins for P02679 (Homo sapiens)
Explore P02679 
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PHAROS:  P02679
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
FIBRIN GH4Homo sapiensMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
FIBRIN IJ4Homo sapiensMutation(s): 0 
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Oligosaccharides

Help

Entity ID: 6
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
K
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.30 Å
  • R-Value Free: 0.290 
  • R-Value Work: 0.220 
  • Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 83.443α = 90
b = 95.6β = 90.19
c = 113.641γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
X-PLORmodel building
X-PLORrefinement
X-PLORphasing

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1998-10-14
    Type: Initial release
  • Version 1.1: 2008-03-10
    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: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary