1N86

Crystal structure of human D-dimer from cross-linked fibrin complexed with GPR and GHRPLDK peptide ligands.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.230 

wwPDB Validation   3D Report Full Report



Literature

The crystal structure of fragment double-D from cross-linked lamprey fibrin reveals isopeptide linkages across an unexpected D-D interface.

Yang, Z.Pandi, L.Doolittle, R.F.

(2002) Biochemistry 41: 15610-15617

  • DOI: 10.1021/bi026666i
  • Primary Citation of Related Structures:  
    1N73, 1N86, 1N8E

  • PubMed Abstract: 
  • The crystal structure of fragment double-D from factor XIII-cross-linked lamprey fibrin has been determined at 2.9 A resolution. The 180 kDa covalent dimer was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens, but not that ...

    The crystal structure of fragment double-D from factor XIII-cross-linked lamprey fibrin has been determined at 2.9 A resolution. The 180 kDa covalent dimer was cocrystallized with the peptide Gly-His-Arg-Pro-amide, which in many fibrinogens, but not that of lamprey, corresponds to the B-knob exposed by thrombin. The structure was determined by molecular replacement, a recently determined structure of lamprey fragment D being used as a search model. GHRPam was found in both the gamma- and beta-chain holes. Unlike the situation with fragment D, the crystal packing of the cross-linked double-D structure exhibits two different D-D interfaces, each gamma-chain facing gamma-chains on two other molecules. One of these (interface I) involves the asymmetric interface observed in all other D fragments and related structures. The other (interface II) encompasses a completely different set of residues. The two abutments differ in that interface I results in an "in line" arrangement of abutting molecules and the interface II in a "zigzag" arrangement. So far as can be determined (the electron density could only be traced on one side of the cross-links), it is the gamma-chains of the newly observed zigzag units (interface II) that are joined by the reciprocal epsilon-amino-gamma-glutamyl cross-links. Auspiciously, the same novel D-D interface was observed in two lower-resolution crystal structures of human double-D preparations that had been crystallized under unusual circumstances. These observations show that double-D structures are linked in a way that is sufficiently flexible to accommodate different D-D interfaces under different circumstances.


    Related Citations: 
    • Crystal structure of fragment D from lamprey fibrinogen complexed with the peptide Gly-His-Arg-Pro-amide.
      Yang, Z., Spraggon, G., Pandi, L., Everse, S.J., Riley, M., Doolittle, R.F.
      (2002) Biochemistry 41: 10218
    • 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 at San Diego, La Jolla, CA 92093-0634, USA.



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrin alpha/alpha-E chain AD87Homo sapiensMutation(s): 0 
Gene Names: FGA
Find proteins for P02671 (Homo sapiens)
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PHAROS:  P02671
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  • Reference Sequence
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrin beta chain BE328Homo sapiensMutation(s): 0 
Gene Names: FGB
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PHAROS:  P02675
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
Fibrin gamma chain CF324Homo sapiensMutation(s): 0 
Gene Names: FGGPRO2061
Find proteins for P02679 (Homo sapiens)
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PHAROS:  P02679
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
fibrin alpha chain peptide ligand fragment Gly-Pro-Arg GH3N/AMutation(s): 0 
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
fibrin beta chain peptide ligand fragment Gly-His-Arg-Pro-Leu-Asp-Lys IJ7N/AMutation(s): 0 
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Explore P02675 
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Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.20 Å
  • R-Value Free: 0.289 
  • R-Value Work: 0.226 
  • R-Value Observed: 0.230 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.328α = 90
b = 130.093β = 90
c = 298.313γ = 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: 2003-01-07
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Atomic model, Data collection, Derived calculations, Structure summary