3HS4 | pdb_00003hs4

Human carbonic anhydrase II complexed with acetazolamide

• PDB DOI: https://doi.org/10.2210/pdb3HS4/pdb

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


• Deposited: 2009-06-10 Released: 2009-12-08 
• Deposition Author(s): Robbins, A.H., Genis, C., Domsic, J., Sippel, K.H., Agbandje-McKenna, M., McKenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.10 Å
• R-Value Free: 
  0.140 (Depositor), 0.136 (DCC) 
• R-Value Work: 
  0.112 (Depositor), 0.117 (DCC) 
• R-Value Observed: 
  0.113 (Depositor) 

Starting Model: experimental

Literature

High-resolution structure of human carbonic anhydrase II complexed with acetazolamide reveals insights into inhibitor drug design.

Sippel, K.H., Robbins, A.H., Domsic, J., Genis, C., Agbandje-McKenna, M., McKenna, R.

(2009) Acta Crystallogr Sect F Struct Biol Cryst Commun 65: 992-995

• PubMed: 19851004 
• DOI: https://doi.org/10.1107/S1744309109036665
• Primary Citation Related Structures: 
  3HS4


• PubMed Abstract: 
  

  The crystal structure of human carbonic anhydrase II (CA II) complexed with the inhibitor acetazolamide (AZM) has been determined at 1.1 A resolution and refined to an R(cryst) of 11.2% and an R(free) of 14.7%. As observed in previous CA II-inhibitor complexes, AZM binds directly to the zinc and makes several key interactions with active-site residues. The high-resolution data also showed a glycerol molecule adjacent to the AZM in the active site and two additional AZMs that are adventitiously bound on the surface of the enzyme. The co-binding of AZM and glycerol in the active site demonstrate that given an appropriate ring orientation and substituents, an isozyme-specific CA inhibitor may be developed.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, FL 32610, USA.

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: 30.11 kDa 
• Atom Count: 2,536 
• Modeled Residue Count: 257 
• Deposited Residue Count: 260 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 2	A	260	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
AZM	D [auth A], E [auth A], F [auth A]	5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE C4 H6 N4 O3 S2 BZKPWHYZMXOIDC-UHFFFAOYSA-N
GOL	C [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: 1.10 Å
• R-Value Free:  0.140 (Depositor), 0.136 (DCC) 
• R-Value Work:  0.112 (Depositor), 0.117 (DCC) 
• R-Value Observed: 0.113 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.252	α = 90
b = 41.097	β = 104.31
c = 71.82	γ = 90

Software Package:

Software Name	Purpose
SHELXL-97	refinement
CNS	refinement
ADSC	data collection
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2009-12-08 
Deposition Author(s): Robbins, A.H., Genis, C., Domsic, J., Sippel, K.H., Agbandje-McKenna, M., McKenna, R.

Revision History  

• Version 1.0: 2009-12-08
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Non-polymer description, Version format compliance
• Version 1.2: 2019-07-24
  Changes: Data collection, Refinement description
• Version 1.3: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description