Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 3-mer - A1B1C1 

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

Macromolecule Content

• Total Structure Weight: 40.66 kDa 
• Atom Count: 2611 
• Residue Count: 312 
• Unique protein chains: 3

4E05

Anophelin from the malaria vector inhibits thrombin through a novel reverse-binding mechanism

• DOI: 10.2210/pdb4E05/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Homo sapiens, Anopheles albimanus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2012-03-02 Released: 2012-12-05 
• Deposition Author(s): Figueiredo, A.C., de Sanctis, D., Gutierrez-Gallego, R., Cereija, T.B., Macedo-Ribeiro, S., Fuentes-Prior, P., Pereira, P.J.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.201 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 

Literature

Unique thrombin inhibition mechanism by anophelin, an anticoagulant from the malaria vector.

Figueiredo, A.C., de Sanctis, D., Gutierrez-Gallego, R., Cereija, T.B., Macedo-Ribeiro, S., Fuentes-Prior, P., Pereira, P.J.

(2012) Proc Natl Acad Sci U S A 109: E3649-E3658

• PubMed: 23223529 
• DOI: 10.1073/pnas.1211614109
• Primary Citation of Related Structures:  
  4E05, 4E06


• PubMed Abstract: 
  

Anopheles mosquitoes are vectors of malaria, a potentially fatal blood disease affecting half a billion humans worldwide. These blood-feeding insects include in their antihemostatic arsenal a potent thrombin inhibitor, the flexible and cysteine-less anophelin. Here, we present a thorough structure-and-function analysis of thrombin inhibition by anophelin, including the 2.3-Å crystal structure of the human thrombin·anophelin complex. Anophelin residues 32-61 are well-defined by electron density, completely occupying the long cleft between the active site and exosite I. However, in striking contrast to substrates, the D50-R53 anophelin tetrapeptide occupies the active site cleft of the enzyme, whereas the upstream residues A35-P45 shield the regulatory exosite I, defining a unique reverse-binding mode of an inhibitor to the target proteinase. The extensive interactions established, the disruption of thrombin's active site charge-relay system, and the insertion of residue R53 into the proteinase S(1) pocket in an orientation opposed to productive substrates explain anophelin's remarkable specificity and resistance to proteolysis by thrombin. Complementary biophysical and functional characterization of point mutants and truncated versions of anophelin unambiguously establish the molecular mechanism of action of this family of serine proteinase inhibitors (I77). These findings have implications for the design of novel antithrombotics.

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Organizational Affiliation: 

Instituto de Biologia Molecular e Celular (IBMC), Universidade do Porto, 4150-180 Porto, Portugal.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin	L	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	H	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
Salivary anti-thrombin peptide anophelin	I	61	Anopheles albimanus	Mutation(s): 0  Gene Names: anophelin, AT
Find proteins for Q9NJS1 (Anopheles albimanus) Explore Q9NJS1  Go to UniProtKB:  Q9NJS1

Small Molecules

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.30 Å
• R-Value Free: 0.201 
• R-Value Work: 0.169 
• R-Value Observed: 0.171 
• Space Group: P 3₁ 1 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 120.18	α = 90
b = 120.18	β = 90
c = 77.81	γ = 120

Software Package:

Software Name	Purpose
SCALA	data scaling
PHASER	phasing
PHENIX	refinement
PDB_EXTRACT	data extraction
DNA	data collection
XDS	data reduction

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2012-03-02 
• Released Date: 2012-12-05 
Deposition Author(s): Figueiredo, A.C., de Sanctis, D., Gutierrez-Gallego, R., Cereija, T.B., Macedo-Ribeiro, S., Fuentes-Prior, P., Pereira, P.J.B.

Revision History 

• Version 1.0: 2012-12-05
  Type: Initial release
  
• Version 1.1: 2012-12-26
  Changes: Database references
• Version 1.2: 2013-01-09
  Changes: Database references
• Version 1.3: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary