Biological Assembly 1  

 3D View: Structure | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 8-mer - A2B2C2D2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 8-mer - A4B2C1D1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 169.70 kDa 
• Atom Count: 11417 
• Modelled Residue Count: 1414 
• Deposited 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
• Mutation(s): No 


• 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: 2.90 Å
• R-Value Free: 0.318 
• R-Value Work: 0.241 
• R-Value Observed: 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:  
  1FZB, 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

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
PEPTIDE LIGAND GPRG	G, H	4	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	B, E	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	C, F	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.318 
• R-Value Work: 0.241 
• R-Value Observed: 0.241 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 93.82	α = 90
b = 95.5	β = 96.08
c = 113.76	γ = 90

Software Package:

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

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
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Data collection, Database references, Derived calculations, Other, Structure summary