3W6H | pdb_00003w6h

Crystal structure of 19F probe-labeled hCAI in complex with acetazolamide

• PDB DOI: https://doi.org/10.2210/pdb3W6H/pdb

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


• Deposited: 2013-02-14 Released: 2013-03-13 
• Deposition Author(s): Takaoka, Y., Kioi, Y., Morito, A., Otani, J., Arita, K., Ashihara, E., Ariyoshi, M., Tochio, H., Shirakawa, M., Hamachi, I.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free: 
  0.283 (Depositor), 0.281 (DCC) 
• R-Value Work: 
  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 
  0.228 (Depositor) 

Starting Model: experimental

Literature

Quantitative Comparison of Protein Dynamics in Live Cells and In Vitro by In-Cell 19F-NMR

Takaoka, Y., Kioi, Y., Morito, A., Otani, J., Arita, K., Ashihara, E., Ariyoshi, M., Tochio, H., Shirakawa, M., Hamachi, I.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 58.73 kDa 
• Atom Count: 4,084 
• Modeled Residue Count: 512 
• Deposited Residue Count: 520 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 1	A, B	260	Homo sapiens	Mutation(s): 0  Gene Names: CA1 EC: 4.2.1.1 (PDB Primary Data), 4.2.1.69 (UniProt)
UniProt & NIH Common Fund Data Resources
Find proteins for P00915 (Homo sapiens) Explore P00915  Go to UniProtKB:  P00915
PHAROS:  P00915 GTEx:  ENSG00000133742

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLB	C [auth A], F [auth B]	1-(2-ethoxyethoxy)-3,5-bis(trifluoromethyl)benzene C12 H12 F6 O2 GWAJLKXPMOKZEL-UHFFFAOYSA-N
AZM	E [auth A], H [auth B]	5-ACETAMIDO-1,3,4-THIADIAZOLE-2-SULFONAMIDE C4 H6 N4 O3 S2 BZKPWHYZMXOIDC-UHFFFAOYSA-N
ZN	D [auth A], G [auth B]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
AZM	BindingDB:  3W6H	Ki: min: 0.25, max: 1734 (nM) from 36 assay(s)
		Kd: min: 290, max: 2400 (nM) from 7 assay(s)
		IC50: min: 1, max: 6100 (nM) from 34 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.96 Å
• R-Value Free:  0.283 (Depositor), 0.281 (DCC) 
• R-Value Work:  0.222 (Depositor), 0.220 (DCC) 
• R-Value Observed: 0.228 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 62.039	α = 90
b = 65.28	β = 90
c = 120.485	γ = 90

Software Package:

Software Name	Purpose
ADSC	data collection
PHASER	phasing
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-03-13 
Deposition Author(s): Takaoka, Y., Kioi, Y., Morito, A., Otani, J., Arita, K., Ashihara, E., Ariyoshi, M., Tochio, H., Shirakawa, M., Hamachi, I.

Revision History  

• Version 1.0: 2013-03-13
  Type: Initial release
  
• Version 1.1: 2023-11-08
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-10-16
  Changes: Structure summary