3K7K | pdb_00003k7k

Crystal structure of the complex between Carbonic Anhydrase II and anions


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free: 
    0.248 (Depositor), 0.199 (DCC) 
  • R-Value Work: 
    0.194 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 
    0.197 (Depositor) 

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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This is version 1.3 of the entry. See complete history

Literature

Carbonic anhydrase inhibitors. X-ray crystal studies of the carbonic anhydrase II-trithiocarbonate adduct-An inhibitor mimicking the sulfonamide and urea binding to the enzyme

Temperini, C.Scozzafava, A.Supuran, C.T.

(2010) Bioorg Med Chem Lett 20: 474-478

  • DOI: https://doi.org/10.1016/j.bmcl.2009.11.124
  • Primary Citation Related Structures: 
    3K7K

  • PubMed Abstract: 

    Trithiocarbonate (CS32-) inhibits with low micromolar affinities several mammalian carbonic anhydrases, CAs, EC 4.2.1.1 [Innocenti et al., Bioorg. Med. Chem. Lett. 2009, 19, 1855]. Here we report the X-ray crystal structure of the hCA II-trithiocarbonate adduct. Trithiocarbonate is monodentately bound to the Zn(II) ion and makes several hydrogen bonds with Thr199 and two water molecules from the enzyme active site. Its binding is different from that of ureate, another small inhibitor isosteric with trithiocarbonate but somehow mimicks the binding of the SO(2)NH moiety present in the sulfonamide inhibitors and is similar to that of bicarbonate. Compounds incorporating this new zinc-binding group, CS2-, may thus lead to new classes of potent inhibitors.


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

Macromolecule Content 

  • Total Structure Weight: 29.67 kDa 
  • Atom Count: 2,299 
  • Modeled Residue Count: 257 
  • Deposited Residue Count: 260 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbonic anhydrase 2260Homo sapiensMutation(s): 0 
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
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Reference Sequence

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.90 Å
  • R-Value Free:  0.248 (Depositor), 0.199 (DCC) 
  • R-Value Work:  0.194 (Depositor), 0.196 (DCC) 
  • R-Value Observed: 0.197 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.07α = 90
b = 41.41β = 104.45
c = 72.23γ = 90
Software Package:
Software NamePurpose
CrysalisProdata collection
AMoREphasing
REFMACrefinement
CrysalisProdata reduction
CrysalisProdata scaling

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2010-01-26
    Type: Initial release
  • Version 1.1: 2011-07-13
    Changes: Version format compliance
  • Version 1.2: 2017-11-01
    Changes: Refinement description
  • Version 1.3: 2023-11-01
    Changes: Data collection, Database references, Derived calculations, Refinement description