2HOD

Crystal Structure of Fragment D from Human Fibrinogen Complexed with Gly-hydroxyPro-Arg-Pro-amide

• PDB DOI:  https://doi.org/10.2210/pdb2HOD/pdb

• Classification: BLOOD CLOTTING/PEPTIDE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2006-07-14 Released: 2007-05-29 
• Deposition Author(s): Doolittle, R.F., Kollman, J.M., Chen, A., Pandi, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.347 
• R-Value Work: 0.268 
• R-Value Observed: 0.238 

Biological Assembly 1  

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

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

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

Biological assembly 2 assigned by authors.

Biological Assembly 3  

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

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

Biological assembly 3 assigned by authors.

Biological Assembly 4  

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

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

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 342.82 kDa 
• Atom Count: 22,278 
• Modelled Residue Count: 2,771 
• Deposited Residue Count: 2,992 
• Unique protein chains: 4

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen alpha chain	A, D, G, J	87	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

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen beta chain	B, E, H, K	328	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

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen, gamma polypeptide	C, F, I, L	323	Homo sapiens	Mutation(s): 0  Gene Names: FGG, PRO2061
UniProt & NIH Common Fund Data Resources
Find proteins for P02679 (Homo sapiens) Explore P02679  Go to UniProtKB:  P02679
PHAROS:  P02679

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Gly-hydroxyPro-Arg-Pro-amide peptide ligand	M, N, O, P, Q, R, S, T	5	N/A	Mutation(s): 0

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	BA [auth H], EA [auth K], U [auth B], X [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
CA	AA [auth F], CA [auth H], DA [auth I], FA [auth K], GA [auth K], HA [auth L], V [auth B], W [auth C], Y [auth E], Z [auth E]	CALCIUM ION Ca BHPQYMZQTOCNFJ-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
HYP	M, N, O, P, Q, R, S, T	L-PEPTIDE LINKING	C5 H9 N O3		PRO

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.90 Å
• R-Value Free: 0.347 
• R-Value Work: 0.268 
• R-Value Observed: 0.238 
• Space Group: P 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 81.647	α = 90
b = 47.069	β = 90.06
c = 431.46	γ = 90

Software Package:

Software Name	Purpose
AMoRE	phasing
CNS	refinement
HKL-2000	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-05-29 
Deposition Author(s): Doolittle, R.F., Kollman, J.M., Chen, A., Pandi, L.

Revision History  

• Version 1.0: 2007-05-29
  Type: Initial release
  
• Version 1.1: 2008-05-01
  Changes: Version format compliance
• Version 1.2: 2011-07-13
  Changes: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 2.1: 2023-08-30
  Changes: Data collection, Database references, Refinement description, Structure summary