6XWZ | pdb_00006xwz

Carbonic Anhydrase II-mediated hydrolysis of selenolester

• PDB DOI: https://doi.org/10.2210/pdb6XWZ/pdb

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


• Deposited: 2020-01-24 Released: 2021-02-03 
• Deposition Author(s): Angeli, A., Feraroni, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free: 
  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.180 (Depositor), 0.190 (DCC) 

Starting Model: experimental

Literature

Selenolesterase enzyme activity of carbonic anhydrases

Angeli, A., Carta, F., Donnini, S., Capperucci, A., Ferraroni, M., Tanini, D., Supuran, C.T.

(2020) Chem Commun (Camb) 

• DOI: https://doi.org/10.1039/D0CC00995D

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: 29.6 kDa 
• Atom Count: 2,233 
• 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 [auth AAA]	260	Homo sapiens	Mutation(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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
GXE (Subject of Investigation/LOI)	D [auth AAA]	benzeneselenol C6 H6 Se WDODWFPDZYSKIA-UHFFFAOYSA-N
GOL	C [auth AAA]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N
ZN	B [auth AAA]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
GXE	BindingDB:  6XWZ	Ki: 490 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.38 Å
• R-Value Free:  0.204 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.180 (Depositor), 0.190 (DCC) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.336	α = 90
b = 41.311	β = 104.259
c = 72.457	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
Aimless	data scaling
REFMAC	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2021-02-03 
Deposition Author(s): Angeli, A., Feraroni, M.

Revision History  

• Version 1.0: 2021-02-03
  Type: Initial release
  
• Version 1.1: 2022-02-16
  Changes: Database references
• Version 1.2: 2024-01-24
  Changes: Data collection, Derived calculations, Refinement description