Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Hetero 10-mer - A2B2C2D2E2 Pseudo Symmetry: Asymmetric - C1 
Pseudo Stoichiometry: Hetero 10-mer - A3B2C2D2E1 

Biological assembly 1 assigned by authors.

Macromolecule Content

• Total Structure Weight: 111.92 kDa 
• Atom Count: 6904 
• Residue Count: 864 
• 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
• Mutation(s): No 


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

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.65 Å
• R-Value Free: 0.290 
• R-Value Observed: 0.221 

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
• Primary Citation of Related Structures:  
  2A45


• 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.

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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 U S A 101: 2718

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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

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
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) 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
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) 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 alpha chain	G, J	57	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: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen beta chain	H, K	91	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: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
Fibrinogen gamma chain	I, L	45	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

Small Molecules

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

Biologically Interesting Molecules (External Reference) 1 Unique

Entity ID: 6
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 
• R-Value Observed: 0.221 
• Space Group: P 3₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 76.263	α = 90
b = 76.263	β = 90
c = 192.452	γ = 120

Software Package:

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

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
  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 1.3: 2013-02-27
  Changes: Other
• Version 1.4: 2017-10-11
  Changes: Advisory, Refinement description
• Version 1.5: 2019-07-24
  Changes: Data collection, Derived calculations, Refinement description
• Version 1.6: 2019-08-14
  Changes: Data collection, Refinement description