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 2.1 of the entry. See complete history. 



Macromolecules
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Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrinogen alpha chain
A, D
197Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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PHAROS:  P02671
GTEx:  ENSG00000171560 
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UniProt GroupP02671
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Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrinogen beta chain
B, E
458Homo sapiensMutation(s): 0 
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PHAROS:  P02675
GTEx:  ENSG00000171564 
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Entity ID: 3
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrinogen gamma chain, isoform gamma-A
C, F
317Homo sapiensMutation(s): 0 
UniProt & NIH Common Fund Data Resources
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PHAROS:  P02679
GTEx:  ENSG00000171557 
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Entity ID: 4
MoleculeChains Sequence LengthOrganismDetailsImage
Fibrin B knob pentapeptideG [auth M],
H [auth N]		5N/AMutation(s): 0 
UniProt
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UniProt GroupP02676
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Oligosaccharides

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Entity ID: 5
MoleculeChains 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-glucopyranoseI [auth G],
J [auth H]		8N-Glycosylation
Glycosylation Resources
GlyTouCan:  G83007AG
GlyCosmos:  G83007AG
GlyGen:  G83007AG
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
  • Version 2.1: 2023-09-06
    Changes: Data collection, Database references, Refinement description, Structure summary