2FOS | pdb_00002fos

Human Carbonic Anhydrase II complexed with two-prong inhibitors

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free: 
    0.153 (Depositor), 0.154 (DCC) 
  • R-Value Work: 
    0.128 (Depositor), 0.137 (DCC) 
  • R-Value Observed: 
    0.127 (Depositor) 

Starting Model: experimental
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This is version 1.5 of the entry. See complete history. 

Literature

Ultrahigh resolution crystal structures of human carbonic anhydrases I and II complexed with two-prong inhibitors reveal the molecular basis of high affinity.

Jude, K.M., Banerjee, A.L., Haldar, M.K., Manokaran, S., Roy, B., Mallik, S., Srivastava, D.K., Christianson, D.W.

(2006) J Am Chem Soc 128: 3011-3018

  • DOI: https://doi.org/10.1021/ja057257n
  • Primary Citation Related Structures: 
    2FOQ, 2FOS, 2FOU, 2FOV, 2FOY

  • PubMed Abstract: 

    The atomic-resolution crystal structures of human carbonic anhydrases I and II complexed with "two-prong" inhibitors are reported. Each inhibitor contains a benzenesulfonamide prong and a cupric iminodiacetate (IDA-Cu(2+)) prong separated by linkers of different lengths and compositions. The ionized NH(-) group of each benzenesulfonamide coordinates to the active site Zn(2+) ion; the IDA-Cu(2+) prong of the tightest-binding inhibitor, BR30, binds to H64 of CAII and H200 of CAI. This work provides the first evidence verifying the structural basis of nanomolar affinity measured for two-prong inhibitors targeting the carbonic anhydrases.

    • Organizational Affiliation: 
    • Roy and Diana Vagelos Laboratories, Department of Chemistry, University of Pennsylvania, Philadelphia, PA 19104, USA.

Macromolecule Content 

  • Total Structure Weight: 30.71 kDa 
  • Atom Count: 2,525 
  • Modeled Residue Count: 259 
  • Deposited Residue Count: 260 
  • Unique protein chains: 1

Macromolecules

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|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Carbonic Anhydrase II260Homo sapiensMutation(s): 1 
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 
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP00918
Sequence Annotations
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Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
CMH
Query on CMH
A
L-PEPTIDE LINKINGC4 H9 Hg N O2 SCYS

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.10 Å
  • R-Value Free:  0.153 (Depositor), 0.154 (DCC) 
  • R-Value Work:  0.128 (Depositor), 0.137 (DCC) 
  • R-Value Observed: 0.127 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 42.444α = 90
b = 41.64β = 104.24
c = 72.278γ = 90
Software Package:
Software NamePurpose
SHELXL-97refinement
SCALEPACKdata scaling
CNSrefinement
HKL-2000data collection
HKL-2000data reduction
CNSphasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2006-04-04
    Type: Initial release
  • Version 1.1: 2008-05-01
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Version format compliance
  • Version 1.3: 2019-07-24
    Changes: Data collection, Derived calculations, Refinement description
  • Version 1.4: 2023-08-30
    Changes: Data collection, Database references, Derived calculations, Refinement description
  • Version 1.5: 2024-11-20
    Changes: Structure summary