2FFD

Fibrinogen Fragment D with "A" knob peptide mimic GPRVVE

• PDB DOI: https://doi.org/10.2210/pdb2FFD/pdb

• Classification: BLOOD CLOTTING
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): No 


• Deposited: 2005-12-19 Released: 2006-07-04 
• Deposition Author(s): Betts, L.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.268 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 

Starting Model: experimental

Literature

The structure of fibrinogen fragment D with the 'A' knob peptide GPRVVE.

Betts, L., Merenbloom, B.K., Lord, S.T.

(2006) Thromb Haemost 4: 1139-1141

• PubMed: 16689770 
• DOI: https://doi.org/10.1111/j.1538-7836.2006.01902.x
• Primary Citation of Related Structures:  
  2FFD

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

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

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B1C1D1 Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Local Symmetry: Cyclic - C2  (Explore in 3D)
Local Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 161.74 kDa 
• Atom Count: 10,894 
• Modelled Residue Count: 1,319 
• Deposited Residue Count: 1,404 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen alpha/alpha-E Chain	A, D	66	Homo sapiens	Mutation(s): 0  Gene Names: FGA
UniProt & NIH Common Fund Data Resources
Find proteins for P02671 (Homo sapiens) Explore P02671  Go to UniProtKB:  P02671
PHAROS:  P02671 GTEx:  ENSG00000171560

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen beta chain	B, E	313	Homo sapiens	Mutation(s): 0  Gene Names: FGB
UniProt & NIH Common Fund Data Resources
Find proteins for P02675 (Homo sapiens) Explore P02675  Go to UniProtKB:  P02675
PHAROS:  P02675 GTEx:  ENSG00000171564
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: P02675-1

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen gamma chain	C, F	311	Homo sapiens	Mutation(s): 0  Gene Names: FGG
UniProt & NIH Common Fund Data Resources
Find proteins for P02679 (Homo sapiens) Explore P02679  Go to UniProtKB:  P02679
PHAROS:  P02679 GTEx:  ENSG00000171557

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
GLY-PRO-ARG-VAL-VAL-GLU peptide	G, H, I, J	6	N/A	Mutation(s): 0

Oligosaccharides

Help

Entity ID: 5
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	K, L	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.89 Å
• R-Value Free: 0.268 
• R-Value Work: 0.211 
• R-Value Observed: 0.214 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.521	α = 90
b = 94.652	β = 90
c = 227.49	γ = 90

Software Package:

Software Name	Purpose
DENZO	data reduction
SCALEPACK	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
AMoRE	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2006-07-04 
Deposition Author(s): Betts, L.

Revision History  

• Version 1.0: 2006-07-04
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.3: 2017-10-18
  Changes: Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary