1FZG

CRYSTAL STRUCTURE OF FRAGMENT D FROM HUMAN FIBRINOGEN WITH THE PEPTIDE LIGAND GLY-HIS-ARG-PRO-AMIDE

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 

wwPDB Validation   3D Report Full Report


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


Literature

Conformational changes in fragments D and double-D from human fibrin(ogen) upon binding the peptide ligand Gly-His-Arg-Pro-amide.

Everse, S.J., Spraggon, G., Veerapandian, L., Doolittle, R.F.

(1999) Biochemistry 38: 2941-2946

  • DOI: 10.1021/bi982626w
  • Primary Citation of Related Structures:  
    1FZE, 1FZF, 1FZG

  • PubMed Abstract: 

    • The structure of fragment double-D from human fibrin has been solved in the presence and absence of the peptide ligands that simulate the two knobs exposed by the removal of fibrinopeptides A and B, respectively. All told, six crystal structures have been determined, three of which are reported here for the first time: namely, fragments D and double-D with the peptide GHRPam alone and double-D in the absence of any peptide ligand ...

    The structure of fragment double-D from human fibrin has been solved in the presence and absence of the peptide ligands that simulate the two knobs exposed by the removal of fibrinopeptides A and B, respectively. All told, six crystal structures have been determined, three of which are reported here for the first time: namely, fragments D and double-D with the peptide GHRPam alone and double-D in the absence of any peptide ligand. Comparison of the structures has revealed a series of conformational changes that are brought about by the various knob-hole interactions. Of greatest interest is a moveable "flap" of two negatively charged amino acids (Glubeta397 and Aspbeta398) whose side chains are pinned back to the coiled coil with a calcium atom bridge until GHRPam occupies the beta-chain pocket. Additionally, in the absence of the peptide ligand GPRPam, GHRPam binds to the gamma-chain pocket, a new calcium-binding site being formed concomitantly.

    Organizational Affiliation: 

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



Macromolecules
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Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
FIBRINOGENA, D87Homo sapiensMutation(s): 0 
Gene Names: FGA
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PHAROS:  P02671
GTEx:  ENSG00000171560 
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UniProt GroupP02671
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Entity ID: 2
MoleculeChainsSequence LengthOrganismDetailsImage
FIBRINOGENB, E328Homo sapiensMutation(s): 0 
Gene Names: FGB
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GTEx:  ENSG00000171564 
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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
FIBRINOGENC, F319Homo sapiensMutation(s): 0 
Gene Names: FGG, PRO2061
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PHAROS:  P02679
GTEx:  ENSG00000171557 
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
FIBRINOGENI [auth M],
J [auth N],
G [auth S],
H [auth T]		4Homo sapiensMutation(s): 0 
Gene Names: FGB
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Find proteins for P02675 (Homo sapiens)
Explore P02675 
Go to UniProtKB:  P02675
PHAROS:  P02675
GTEx:  ENSG00000171564 
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Oligosaccharides

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Entity ID: 5
MoleculeChainsChain Length2D DiagramGlycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranoseK [auth G],
L [auth H]		2N-Glycosylation Oligosaccharides Interaction
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.50 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.233 
  • R-Value Observed: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 54.8α = 90
b = 149.4β = 90
c = 234.7γ = 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  (Full details and data files)

  • Version 1.0: 1999-06-08
    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, Derived calculations, Structure summary