4QY3 | pdb_00004qy3

THE CRYSTAL STRUCTURE OF THE COMPLEX of HCAII WITH AN ORTHO-SUBSTITUTED BENZOIC ACID

• PDB DOI: https://doi.org/10.2210/pdb4QY3/pdb

• Classification: Lyase/Lyase inhibitor
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2014-07-23 Released: 2014-12-03 
• Deposition Author(s): D'Ambrosio, K., De Simone, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.184 (Depositor), 0.178 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.159 (DCC) 

Starting Model: experimental

Literature

Out of the active site binding pocket for carbonic anhydrase inhibitors.

D'Ambrosio, K., Carradori, S., Monti, S.M., Buonanno, M., Secci, D., Vullo, D., Supuran, C.T., De Simone, G.

(2014) Chem Commun (Camb) 51: 302-305

• PubMed: 25407638 
• DOI: https://doi.org/10.1039/c4cc07320g
• Primary Citation Related Structures: 
  4QY3


• PubMed Abstract: 
  

  A structural study of the adduct which 2-benzylsulfinylbenzoic acid forms with human carbonic anhydrase II is reported, showing a binding mode completely different from any other class of carbonic anhydrase inhibitors investigated so far; this carboxylate binds in a pocket situated out of the enzyme active site.

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Organizational Affiliation: 
• Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 16, 80134, Naples, Italy. [e-mail] [e-mail].

Biological Assembly 1  

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

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

Macromolecule Content 

• Total Structure Weight: 29.82 kDa 
• Atom Count: 2,414 
• Modeled Residue Count: 257 
• Deposited Residue Count: 259 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	259	Homo sapiens	Mutation(s): 0  Gene Names: CA2 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00918 (Homo sapiens) Explore P00918  Go to UniProtKB:  P00918
PHAROS:  P00918 GTEx:  ENSG00000104267

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
HGB	D [auth A]	4-(HYDROXYMERCURY)BENZOIC ACID C7 H6 Hg O3 WMHRYLDWLOGHSG-UHFFFAOYSA-M
3G1	C [auth A]	2-[(S)-benzylsulfinyl]benzoic acid C14 H12 O3 S IHSDWNKZUMUWEX-SFHVURJKSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.184 (Depositor), 0.178 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.159 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.15	α = 90
b = 41.53	β = 104.52
c = 72.18	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-12-03 
Deposition Author(s): D'Ambrosio, K., De Simone, G.

Revision History  

• Version 1.0: 2014-12-03
  Type: Initial release
  
• Version 1.1: 2014-12-17
  Changes: Database references
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description