3H32

Crystal structure of D-dimer from human fibrin complexed with Gly-His-Arg-Pro-Tyr-amide

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 

wwPDB Validation   3D Report Full Report


This is version 2.0 of the entry. See complete history. 


Literature

Two families of synthetic peptides that enhance fibrin turbidity and delay fibrinolysis by different mechanisms.

Pandi, L., Kollman, J.M., Lopez-Lira, F., Burrows, J.M., Riley, M., Doolittle, R.F.

(2009) Biochemistry 48: 7201-7208

  • DOI: 10.1021/bi900647g
  • Primary Citation of Related Structures:  
    3H32

  • PubMed Abstract: 

    • When fibrin clots are formed in vitro in the presence of certain positively charged peptides, the turbidity is enhanced and fibrinolysis is delayed. Here we show that these two phenomena are not always linked and that different families of peptides bring about the delay of lysis in different ways ...

    When fibrin clots are formed in vitro in the presence of certain positively charged peptides, the turbidity is enhanced and fibrinolysis is delayed. Here we show that these two phenomena are not always linked and that different families of peptides bring about the delay of lysis in different ways. In the case of intrinsically adhesive peptides corresponding to certain regions of the fibrinogen gammaC and betaC domains, even though these peptides bind to fibrin(ogen) and enhance turbidity, the delay in lysis is mainly due to direct inhibition of plasminogen activation. In contrast, for certain pentapeptides patterned on fibrin B knobs, the delay in lysis is a consequence of how fibrin units assemble. On their own, these B knob surrogates can induce the gelation of fibrinogen molecules. The likely cause of enhanced clot turbidity and delay in fibrinolysis was revealed by a crystal structure of the D-dimer from human fibrinogen cocrystallized with GHRPYam, the packing of which showed the direct involvement of the ligand tyrosines in antiparallel betaC-betaC interactions.

    Organizational Affiliation: 

    Department of Chemistry and Biochemistry and Division of Biology, University of California at San Diego, La Jolla, California 92093-0314, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen alpha chain A, D197Homo sapiensMutation(s): 0 
Gene Names: FGA
Find proteins for P02671 (Homo sapiens)
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Go to UniProtKB:  P02671
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PHAROS:  P02671
GTEx:  ENSG00000171560
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen beta chain B, E458Homo sapiensMutation(s): 0 
Gene Names: FGB
Find proteins for P02675 (Homo sapiens)
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Go to UniProtKB:  P02675
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PHAROS:  P02675
GTEx:  ENSG00000171564
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrinogen gamma chain, isoform gamma-A C, F317Homo sapiensMutation(s): 0 
Gene Names: FGG, PRO2061
Find proteins for P02679 (Homo sapiens)
Explore P02679 
Go to UniProtKB:  P02679
NIH Common Fund Data Resources
PHAROS:  P02679
GTEx:  ENSG00000171557
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  • Reference Sequence
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrin B knob pentapeptide M, N5N/AMutation(s): 0 
Find proteins for P02676 (Bos taurus)
Explore P02676 
Go to UniProtKB:  P02676
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  • Reference Sequence
Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
N-acetyl-alpha-neuraminic acid-(2-6)-beta-D-galactopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-2)-alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
G, H
8 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.60 Å
  • R-Value Free: 0.320 
  • R-Value Work: 0.263 
  • R-Value Observed: 0.263 
  • Space Group: C 1 2 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 264.72α = 90
b = 97.32β = 122.78
c = 132.49γ = 90
Software Package:
Software NamePurpose
ADSCdata collection
AMoREphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2009-07-28
    Type: Initial release
  • Version 1.1: 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, Derived calculations, Structure summary