Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 5-mer - A2B2C1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 69.65 kDa 
• Atom Count: 4807 
• Modelled Residue Count: 576 
• Deposited Residue Count: 604 
• Unique protein chains: 3

2HWL

Crystal structure of thrombin in complex with fibrinogen gamma' peptide

• DOI: 10.2210/pdb2HWL/pdb

• Classification: HYDROLASE
• Organism(s): Homo sapiens
• Expression System: Cricetulus griseus
• Mutation(s): Yes 


• Deposited: 2006-08-01 Released: 2006-09-19 
• Deposition Author(s): Pineda, A.O., Chen, Z.W., Marino, F., Mathews, F.S., Mosesson, M.W., Di Cera, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 

Literature

Crystal structure of thrombin in complex with fibrinogen gamma' peptide.

Pineda, A.O., Chen, Z.W., Marino, F., Mathews, F.S., Mosesson, M.W., Di Cera, E.

(2007) Biophys Chem 125: 556-559

• PubMed: 16962697 
• DOI: 10.1016/j.bpc.2006.08.005
• Primary Citation of Related Structures:  
  2HWL


• PubMed Abstract: 
  

Elevated levels of heterodimeric gamma(A)/gamma' fibrinogen 2 have been associated with an increased incidence of coronary artery disease, whereas a lowered content of gamma' chains is associated with an increased risk of venous thrombosis. Both situations may be related to the unique features of thrombin binding to variant gamma' chains. The gamma' peptide is an anionic fragment that binds thrombin with high affinity without interfering directly with substrate binding. Here we report the crystal structure of thrombin bound to the gamma' peptide, solved at 2.4 A resolution. The complex reveals extensive interactions between thrombin and the gamma' peptide mediated by electrostatic contacts with residues of exosite II and hydrophobic interactions with a pocket in close proximity to the Na(+) binding site. In its binding mode, the gamma' peptide completely overlaps with heparin bound to exosite II. These findings are consistent with functional data and broaden our understanding of how thrombin interacts with fibrinogen at the molecular level.

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Organizational Affiliation: 

Department of Pathochemistry, German Cancer Research Center, 69120 Heidelberg, Germany.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	A, C	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Prothrombin	B, D	259	Homo sapiens	Mutation(s): 1  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
NIH Common Fund Data Resources
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen gamma' peptide	E [auth P]	14	N/A	Mutation(s): 2
Find proteins for P02679 (Homo sapiens) Explore P02679  Go to UniProtKB:  P02679
NIH Common Fund Data Resources
PHAROS:  P02679 GTEx:  ENSG00000171557

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
NAG	G [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	F [auth B], H [auth D]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
PTR	E [auth P]	L-PEPTIDE LINKING	C9 H12 N O6 P		TYR

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 0.249 
• R-Value Work: 0.214 
• R-Value Observed: 0.214 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 66.397	α = 90
b = 81.523	β = 109.35
c = 70.256	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2006-08-01 
• Released Date: 2006-09-19 
Deposition Author(s): Pineda, A.O., Chen, Z.W., Marino, F., Mathews, F.S., Mosesson, M.W., Di Cera, E.

Revision History  

• Version 1.0: 2006-09-19
  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: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Database references, Derived calculations, Structure summary