Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 10-mer - A4B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A4B2C1D1E1F1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 171.36 kDa 
• Atom Count: 10713 
• Residue Count: 1313 
• Unique protein chains: 4

1FZG

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

• DOI: 10.2210/pdb1FZG/pdb

• Classification: BLOOD COAGULATION
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 1999-01-01 Released: 1999-06-08 
• Deposition Author(s): Everse, S.J., Spraggon, G., Veerapandian, L., Doolittle, R.F.

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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 

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

• PubMed: 10074346 
• DOI: 10.1021/bi982626w
• Primary Citation of Related Structures:  
  1FZG, 1FZF, 1FZE


• 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. 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.

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Organizational Affiliation: 

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

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
FIBRINOGEN	A, D	87	Homo sapiens	Mutation(s): 0  Gene Names: FGA
Find proteins for P02671 (Homo sapiens) Explore P02671  Go to UniProtKB:  P02671
NIH Common Fund Data Resources
PHAROS:  P02671 GTEx:  ENSG00000171560

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
FIBRINOGEN	B, E	328	Homo sapiens	Mutation(s): 0  Gene Names: FGB
Find proteins for P02675 (Homo sapiens) Explore P02675  Go to UniProtKB:  P02675
NIH Common Fund Data Resources
PHAROS:  P02675 GTEx:  ENSG00000171564

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
FIBRINOGEN	C, F	319	Homo sapiens	Mutation(s): 0  Gene Names: FGG, PRO2061
Find proteins for P02679 (Homo sapiens) Explore P02679  Go to UniProtKB:  P02679
NIH Common Fund Data Resources
PHAROS:  P02679 GTEx:  ENSG00000171557

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
FIBRINOGEN	M, N, S, T	4	Homo sapiens	Mutation(s): 0  Gene Names: FGB
Find proteins for P02675 (Homo sapiens) Explore P02675  Go to UniProtKB:  P02675
NIH Common Fund Data Resources
PHAROS:  P02675 GTEx:  ENSG00000171564

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Chain Length	2D Diagram	Glycosylation
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H	2		N-Glycosylation

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
CA	B, C, E, F	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

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 = 54.8	α = 90
b = 149.4	β = 90
c = 234.7	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
X-PLOR	model building
X-PLOR	refinement
X-PLOR	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1999-01-01 
• Released Date: 1999-06-08 
Deposition Author(s): Everse, S.J., Spraggon, G., Veerapandian, L., Doolittle, R.F.

Revision History 

• 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