Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Standalone Viewers  
Protein Workshop | Ligand Explorer

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 111917.71 
• Atom Count: 6904 
• Residue Count: 976 
• Unique protein chains: 5

2A45

Crystal structure of the complex between thrombin and the central "E" region of fibrin

• DOI: 10.2210/pdb2A45/pdb
• Entry 2A45 supersedes 1QVH

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens


• Deposited: 2005-06-27 Released: 2006-05-02 
• Deposition Author(s): Pechik, I., Madrazo, J., Gilliland, G.L., Medved, L.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.65 Å
• R-Value Free: 0.290 

Literature

Structural basis for sequential cleavage of fibrinopeptides upon fibrin assembly.

Pechik, I., Yakovlev, S., Mosesson, M.W., Gilliland, G.L., Medved, L.

(2006) Biochemistry 45: 3588-3597

• PubMed: 16533041 
• DOI: 10.1021/bi0525369


• PubMed Abstract: 
  

Nonsubstrate interaction of thrombin with fibrinogen promotes sequential cleavage of fibrinopeptides A and B (fpA and fpB, respectively) from the latter, resulting in its conversion into fibrin. The recently established crystal structure of human thrombin in complex with the central part of human fibrin clarified the mechanism of this interaction. Here, we reveal new details of the structure and present the results of molecular modeling of the fpA- and fpB-containing portions of the Aalpha and Bbeta chains, not identified in the complex, in both fibrinogen and protofibrils. The analysis of the results reveals that in fibrinogen the fpA-containing portions are in a more favorable position to bind in the active site cleft of bound thrombin. Surface plasmon resonance experiments establish that the fpB-containing portions interact with the fibrin-derived dimeric D-D fragment, suggesting that in protofibrils they bind to the newly formed DD regions bringing fpB into the vicinity of bound thrombin. These findings provide a coherent rationale for the preferential removal of fpA from fibrinogen at the first stage of fibrin assembly and the accelerated cleavage of fpB from protofibrils and/or fibrils at the second stage.

---

Related Citations: 

• Crystal Structure of the Complex between Thrombin and the Central "E" Region of Fibrin
  Pechik, I.,Madrazo, J.,Mosesson, M.W.,Hernandez, I.,Gilliland, G.L.,Medved, L.
  (2004) Proc.Natl.Acad.Sci.USA 101: 2718




---

Organizational Affiliation: 

Center for Advanced Research in Biotechnology, University of Maryland Biotechnology Institute and National Institute of Standards and Technology, Rockville, Maryland 20850, USA.

Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Thrombin light chain	A, D	36	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details
Thrombin heavy chain	B, E	259	Homo sapiens	Mutation(s): 0  Gene Names: F2 EC: 3.4.21.5
Find proteins for P00734 (Homo sapiens) Go to Gene View: F2 Go to UniProtKB:  P00734

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details
Fibrinogen alpha chain	G, J	57	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: 4
Molecule	Chains	Sequence Length	Organism	Details
Fibrinogen beta chain	H, K	91	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: 5
Molecule	Chains	Sequence Length	Organism	Details
Fibrinogen gamma chain	I, L	45	Homo sapiens	Mutation(s): 0  Gene Names: FGG
Find proteins for P02679 (Homo sapiens) Go to Gene View: FGG Go to UniProtKB:  P02679

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram & Interactions
PO4	B, E	PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K
0G6	B, E	D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide PPACK C21 H34 Cl N6 O3 DVFLYEYCMMLBTQ-VSZNYVQBSA-O

Biologically Interesting Molecules 1 Unique
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_000020 (0G6)	B,E	D-Phe-Pro-Arg-CH2Cl	Peptide-like / Inhibitor		--

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.65 Å
• R-Value Free: 0.290 
• Space Group: P 3₁

Unit Cell:

Length (Å)	Angle (°)
a = 76.263	α = 90.00
b = 76.263	β = 90.00
c = 192.452	γ = 120.00

Software Package:

Software Name	Purpose
CNS	phasing
d*TREK	data reduction
SHELXL-97	refinement
CNS	refinement
d*TREK	data scaling

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2005-06-27 
• Released Date: 2006-05-02 
• Deposition Author(s): Pechik, I., Madrazo, J., Gilliland, G.L., Medved, L.
• This entry supersedes: 1QVH

Revision History 

• Version 1.0: 2006-05-02
  Type: Initial release
• Version 1.1: 2008-04-30
  Type: Version format compliance
• Version 1.2: 2011-07-13
  Type: Atomic model, Database references, Derived calculations, Non-polymer description, Structure summary, Version format compliance
• Version 1.3: 2013-02-27
  Type: Other
• Version 1.4: 2017-10-11
  Type: Advisory, Refinement description