6CJV | pdb_00006cjv

Carbonic anhydrase IX-mimic in complex with sucralose

• PDB DOI: https://doi.org/10.2210/pdb6CJV/pdb

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


• Deposited: 2018-02-26 Released: 2018-08-08 
• Deposition Author(s): Lomelino, C.L., Murray, A.B., McKenna, R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free: 
  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work: 
  0.162 (Depositor), 0.164 (DCC) 
• R-Value Observed: 
  0.163 (Depositor) 

Starting Model: experimental

Literature

Sweet Binders: Carbonic Anhydrase IX in Complex with Sucralose.

Lomelino, C.L., Murray, A.B., Supuran, C.T., McKenna, R.

(2018) ACS Med Chem Lett 9: 657-661

• PubMed: 30034596 
• DOI: https://doi.org/10.1021/acsmedchemlett.8b00100
• Primary Citation Related Structures: 
  6CJV


• PubMed Abstract: 
  

  Carbonic anhydrase IX (CA IX) expression is important for the regulation of pH in hypoxic tumors and is emerging as a therapeutic target for the treatment of various cancers. Recent studies have demonstrated the selectivity of sucrose, saccharin, and acesulfame potassium for CA IX over other CA isoforms. Reported here is the X-ray crystal structure of CA IX-mimic in complex with sucralose determined to ∼1.5 Å resolution. Furthermore, this structure is compared to the aforementioned sweetener/carbohydrate structural studies in order to determine active site properties of CA IX that promote selective binding. This structural analysis provides a further understanding of CA IX isoform specific inhibition to facilitate the design of new inhibitors and anticancer drugs.

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Organizational Affiliation: 
• Department of Biochemistry and Molecular Biology, College of Medicine, University of Florida, Gainesville, Florida 32610, United States.
University of Florence, NEUROFARBA Department, Sezione di Farmaceutica e Nutraceutica, Via Ugo Schiff 6, 50019 Sesto Fiorentino (Florence), Italy.

Biological Assembly 1  

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

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

Biological Assembly Evidence: isothermal titration calorimetry

Macromolecule Content 

• Total Structure Weight: 29.31 kDa 
• Atom Count: 2,285 
• 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

Oligosaccharides

Help  

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
4-chloro-4-deoxy-alpha-D-galactopyranose-(1-2)-1,6-dichloro-1,6-dideoxy-beta-D-fructofuranose	B	2	N/A	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ZN	C [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Biologically Interesting Molecules (External Reference) 

1 Unique

Entity ID: 2
ID	Chains	Name	Type/Class	2D Diagram	3D Interactions
PRD_900090	B	sucralose	Oligosaccharide / Substrate analog

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.55 Å
• R-Value Free:  0.185 (Depositor), 0.180 (DCC) 
• R-Value Work:  0.162 (Depositor), 0.164 (DCC) 
• R-Value Observed: 0.163 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 41.82	α = 90
b = 41.446	β = 103.97
c = 71.74	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
PHENIX	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2018-08-08 
Deposition Author(s): Lomelino, C.L., Murray, A.B., McKenna, R.

Revision History  

• Version 1.0: 2018-08-08
  Type: Initial release
  
• Version 2.0: 2020-04-22
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Structure summary
• Version 3.1: 2023-10-04
  Changes: Advisory, Data collection, Database references, Refinement description