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: 2.5 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.233 

wwPDB Validation 3D Report Full Report


This is version 1.2 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:  

  • 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 ...

    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

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
FIBRINOGEN
A, D
87Homo sapiensMutation(s): 0 
Gene Names: FGA
Find proteins for P02671 (Homo sapiens)
Go to Gene View: FGA
Go to UniProtKB:  P02671
Entity ID: 2
MoleculeChainsSequence LengthOrganismDetails
FIBRINOGEN
B, E
328Homo sapiensMutation(s): 0 
Gene Names: FGB
Find proteins for P02675 (Homo sapiens)
Go to Gene View: FGB
Go to UniProtKB:  P02675
Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
FIBRINOGEN
C, F
319Homo sapiensMutation(s): 0 
Gene Names: FGG
Find proteins for P02679 (Homo sapiens)
Go to Gene View: FGG
Go to UniProtKB:  P02679
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
FIBRINOGEN
S, T, M, N
4Homo sapiensMutation(s): 0 
Gene Names: FGB
Find proteins for P02675 (Homo sapiens)
Go to Gene View: FGB
Go to UniProtKB:  P02675
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA
Download SDF File 
Download CCD File 
B, C, E, F
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
NAG
Query on NAG
Download SDF File 
Download CCD File 
B, E
N-ACETYL-D-GLUCOSAMINE
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.302 
  • R-Value Work: 0.233 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 54.800α = 90.00
b = 149.400β = 90.00
c = 234.700γ = 90.00
Software Package:
Software NamePurpose
SCALEPACKdata scaling
X-PLORphasing
X-PLORmodel building
X-PLORrefinement
DENZOdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History 

  • Version 1.0: 1999-06-08
    Type: Initial release
  • Version 1.1: 2008-03-10
    Type: Version format compliance
  • Version 1.2: 2011-07-13
    Type: Non-polymer description, Version format compliance