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 

Starting Model: experimental
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This is version 2.1 of the entry. See complete history


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: https://doi.org/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 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.


  • 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
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrin alpha/alpha-E chain
A, D
87Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02671 (Homo sapiens)
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Go to UniProtKB:  P02671
PHAROS:  P02671
GTEx:  ENSG00000171560 
Entity Groups  
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UniProt GroupP02671
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  • Reference Sequence
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrin beta chain
B, E
328Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02675 (Homo sapiens)
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Go to UniProtKB:  P02675
PHAROS:  P02675
GTEx:  ENSG00000171564 
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UniProt GroupP02675
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrin gamma chain
C, F
324Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
Find proteins for P02679 (Homo sapiens)
Explore P02679 
Go to UniProtKB:  P02679
PHAROS:  P02679
GTEx:  ENSG00000171557 
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UniProt GroupP02679
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  • Reference Sequence

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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
fibrin alpha chain peptide ligand fragment Gly-Pro-Arg
G, H
3N/AMutation(s): 0 
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PHAROS:  P02671
GTEx:  ENSG00000171560 
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UniProt GroupP02671
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Entity ID: 5
MoleculeChains Sequence LengthOrganismDetailsImage
fibrin beta chain peptide ligand fragment Gly-His-Arg-Pro-Leu-Asp-Lys
I, J
7N/AMutation(s): 0 
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Find proteins for P02675 (Homo sapiens)
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Go to UniProtKB:  P02675
PHAROS:  P02675
GTEx:  ENSG00000171564 
Entity Groups  
UniProt GroupP02675
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  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NDG
Query on NDG

Download Ideal Coordinates CCD File 
K [auth B],
O [auth E],
R [auth I],
S [auth J]
2-acetamido-2-deoxy-alpha-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-PVFLNQBWSA-N
MAN
Query on MAN

Download Ideal Coordinates CCD File 
L [auth B]alpha-D-mannopyranose
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
CA
Query on CA

Download Ideal Coordinates CCD File 
M [auth B],
N [auth C],
P [auth E],
Q [auth F]
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
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  (Full details and data files)

  • 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
  • Version 2.1: 2023-08-16
    Changes: Data collection, Database references, Refinement description, Structure summary