2IT4 | pdb_00002it4

X ray structure of the complex between Carbonic Anhydrase I and the phosphonate antiviral drug foscarnet

• PDB DOI: https://doi.org/10.2210/pdb2IT4/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2006-10-19 Released: 2007-09-11 
• Deposition Author(s): Temperini, C., Innocenti, A., Guerri, A., Scozzafava, A., Supuran, C.T.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.316 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.246 (Depositor) 
• R-Value Observed: 
  0.249 (Depositor) 

Starting Model: experimental

Literature

Phosph(on)ate as a zinc-binding group in metalloenzyme inhibitors: X-ray crystal structure of the antiviral drug foscarnet complexed to human carbonic anhydrase I.

Temperini, C., Innocenti, A., Guerri, A., Scozzafava, A., Rusconi, S., Supuran, C.T.

(2007) Bioorg Med Chem Lett 17: 2210-2215

• PubMed: 17314045 
• DOI: https://doi.org/10.1016/j.bmcl.2007.01.113
• Primary Citation Related Structures: 
  2IT4


• PubMed Abstract: 
  

  Foscarnet (phosphonoformate trisodium salt), an antiviral used for the treatment of HIV and herpes virus infections, also acts as an activator or inhibitor of the metalloenzyme carbonic anhydrase (CA, EC 4.2.1.1). Interaction of the drug with 11 CA isozymes has been investigated kinetically, and the X-ray structure of its adduct with isoform I (hCA I-foscarnet complex) has been resolved. The first CA inhibitor possessing a phosphonate zinc-binding group is thus evidenced, together with the factors governing recognition of such small molecules by a metalloenzyme active site. Foscarnet is also a clear-cut example of modulator of an enzyme activity which can act either as an activator or inhibitor of a CA isozyme.

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Organizational Affiliation: 
• Università degli Studi di Firenze, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, I-50019 Sesto Fiorentino (Florence), Italy.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 57.07 kDa 
• Atom Count: 4,385 
• Modeled Residue Count: 512 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 1	A, B	256	Homo sapiens	Mutation(s): 0  EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00915 (Homo sapiens) Explore P00915  Go to UniProtKB:  P00915
PHAROS:  P00915 GTEx:  ENSG00000133742

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PPF	D [auth A]	PHOSPHONOFORMIC ACID C H3 O5 P ZJAOAACCNHFJAH-UHFFFAOYSA-N
ZN	C [auth A], E [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.316 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.246 (Depositor) 
• R-Value Observed: 0.249 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.58	α = 90
b = 69.51	β = 90
c = 120.44	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
AMoRE	phasing
REFMAC	refinement
CrysalisPro	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2007-09-11 
Deposition Author(s): Temperini, C., Innocenti, A., Guerri, A., Scozzafava, A., Supuran, C.T.

Revision History  

• Version 1.0: 2007-09-11
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-10-18
  Changes: Refinement description
• Version 1.3: 2018-01-31
  Changes: Experimental preparation
• Version 1.4: 2018-04-04
  Changes: Data collection
• Version 1.5: 2023-08-30
  Changes: Data collection, Database references, Derived calculations, Refinement description