5CLU | pdb_00005clu

THE CRYSTAL STRUCTURE OF THE COMPLEX of HCAII WITH A SACCHARINE DERIVATIVE

• PDB DOI: https://doi.org/10.2210/pdb5CLU/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2015-07-16 Released: 2015-11-11 
• Deposition Author(s): D'Ambrosio, K., De Simone, G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.186 (Depositor), 0.191 (DCC) 
• R-Value Work: 
  0.160 (Depositor), 0.167 (DCC) 

Starting Model: experimental

Literature

A Combined Crystallographic and Theoretical Study Explains the Capability of Carboxylic Acids to Adopt Multiple Binding Modes in the Active Site of Carbonic Anhydrases.

Langella, E., D'Ambrosio, K., D'Ascenzio, M., Carradori, S., Monti, S.M., Supuran, C.T., De Simone, G.

(2016) Chemistry 22: 97-100

• PubMed: 26507456 
• DOI: https://doi.org/10.1002/chem.201503748
• Primary Citation Related Structures: 
  5CLU


• PubMed Abstract: 
  

  Carboxylates are the least investigated class of inhibitors of carbonic anhydrases (CAs). Here we explain the versatility of binding of these molecules to CAs by examining a new adduct of hCA II with N-carboxymethyl-saccharin.

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Organizational Affiliation: 
• Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli (Italy).
Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli (Italy). [e-mail].
Target Discovery Institute, University of Oxford, NDM Research Building, Roosevelt Drive, Headington, Oxford OX3 7FZ (UK).
Department of Pharmacy, "G. D'Annunzio" University of Chieti, Via dei Vestini 31, 66100 Chieti (Italy).
Università degli Studi di Firenze, Polo Scientifico, Laboratorio di Chimica Bioinorganica, Rm. 188, Via della Lastruccia 3, 50019 Sesto Fiorentino, Florence (Italy).
NEUROFARBA Department, Sezione di Scienze Farmaceutiche, Via Ugo Schiff 6, 50019 Sesto Fiorentino, Florence (Italy).
Istituto di Biostrutture e Bioimmagini-CNR, via Mezzocannone 16, 80134 Napoli (Italy). [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: 29.33 kDa 
• Atom Count: 2,396 
• Modeled Residue Count: 257 
• Deposited Residue Count: 257 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	257	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
S8A	C [auth A]	(1,1-dioxido-3-oxo-1,2-benzothiazol-2(3H)-yl)acetic acid C9 H7 N O5 S MQAZHTHFEBUHCD-UHFFFAOYSA-N
GOL	D [auth A]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.186 (Depositor), 0.191 (DCC) 
• R-Value Work:  0.160 (Depositor), 0.167 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.37	α = 90
b = 41.07	β = 104.23
c = 72.06	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-11-11 
Deposition Author(s): D'Ambrosio, K., De Simone, G.

Revision History  

• Version 1.0: 2015-11-11
  Type: Initial release
  
• Version 1.1: 2016-01-27
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Refinement description