4E06

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

• PDB DOI: https://doi.org/10.2210/pdb4E06/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: 3.20 Å
• R-Value Free: 0.208 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 

Biological Assembly 1  

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: 2,512 
• Modelled Residue Count: 308 
• Deposited Residue Count: 356 
• Unique protein chains: 3

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin	A [auth L]	36	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Thrombin	B [auth H]	259	Homo sapiens	Mutation(s): 0  EC: 3.4.21.5
UniProt & NIH Common Fund Data Resources
Find proteins for P00734 (Homo sapiens) Explore P00734  Go to UniProtKB:  P00734
PHAROS:  P00734 GTEx:  ENSG00000180210

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Salivary anti-thrombin peptide anophelin	C [auth I]	61	Anopheles albimanus	Mutation(s): 0  Gene Names: anophelin
UniProt
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	D [auth H]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
NA	E [auth H]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 0.208 
• R-Value Work: 0.177 
• R-Value Observed: 0.178 
• Space Group: H 3 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 209.659	α = 90
b = 209.659	β = 90
c = 127.412	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

• 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
• Version 1.4: 2023-09-13
  Changes: Data collection, Database references, Refinement description, Structure summary