Biological Assembly 1  

 3D View: Structure | Ligand Interaction

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Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 6-mer - A2B2C2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 6-mer -A4B2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 169696.03 
• Atom Count: 11417 
• Residue Count: 1476 
• Unique protein chains: 4

1FZB

CRYSTAL STRUCTURE OF CROSSLINKED FRAGMENT D

• DOI: 10.2210/pdb1FZB/pdb

• Classification: BLOOD COAGULATION
• Organism(s): Homo sapiens


• Deposited: 1997-08-05 Released: 1997-12-03 
• Deposition Author(s): Spraggon, G., Everse, S.J., Doolittle, R.F.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.318 
• R-Value Work: 0.241 

Literature

Crystal structures of fragment D from human fibrinogen and its crosslinked counterpart from fibrin.

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

(1997) Nature 389: 455-462

• PubMed: 9333233 
• DOI: 10.1038/38947
• Primary Citation of Related Structures:  
  1FZA


• PubMed Abstract: 
  

In blood coagulation, units of the protein fibrinogen pack together to form a fibrin clot, but a crystal structure for fibrinogen is needed to understand how this is achieved. The structure of a core fragment (fragment D) from human fibrinogen has now been determined to 2.9 A resolution. The 86K three-chained structure consists of a coiled-coil region and two homologous globular entitles oriented at approximately 130 degrees to each other. Additionally, the covalently bound dimer of fragment D, known as 'double-D', was isolated from human fibrin, crystallized in the presence of a Gly-Pro-Arg-Pro-amide peptide ligand, which simulates the donor polymerization site, and its structure solved by molecular replacement with the model of fragment D.

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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
Molecule	Chains	Sequence Length	Organism	Details
FIBRINOGEN	A, D	87	Homo sapiens	Mutation(s): 0  Gene Names: FGA
Find proteins for P02671 (Homo sapiens) Go to Gene View: FGA Go to UniProtKB:  P02671

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
FIBRINOGEN	B, E	328	Homo sapiens	Mutation(s): 0  Gene Names: FGB
Find proteins for P02675 (Homo sapiens) Go to Gene View: FGB Go to UniProtKB:  P02675

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
FIBRINOGEN	C, F	319	Homo sapiens	Mutation(s): 0  Gene Names: FGG
Find proteins for P02679 (Homo sapiens) Go to Gene View: FGG Go to UniProtKB:  P02679

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details
PEPTIDE LIGAND GPRG	G, H	4	N/A	Mutation(s): 0
Protein Feature View is not available: No corresponding UniProt sequence found.

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
CA	C, F	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N
NAG	B, E	N-ACETYL-D-GLUCOSAMINE C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.9 Å
• R-Value Free: 0.318 
• R-Value Work: 0.241 
• Space Group: P 1 2₁ 1

Unit Cell:

Length (Å)	Angle (°)
a = 93.820	α = 90.00
b = 95.500	β = 96.08
c = 113.760	γ = 90.00

Software Package:

Software Name	Purpose
X-PLOR	model building
X-PLOR	phasing
X-PLOR	refinement

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 1997-08-05 
• Released Date: 1997-12-03 
• Deposition Author(s): Spraggon, G., Everse, S.J., Doolittle, R.F.

Revision History 

• Version 1.0: 1997-12-03
  Type: Initial release
• Version 1.1: 2008-03-24
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Non-polymer description, Version format compliance