6QNG | pdb_00006qng

Three dimensional structure of human carbonic anhydrase XII in complex with benzenesulfonamide

• PDB DOI: https://doi.org/10.2210/pdb6QNG/pdb

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


• Deposited: 2019-02-11 Released: 2020-03-04 
• Deposition Author(s): Dvinskis, E., Leitans, J., Tars, K.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free: 
  0.250 (Depositor), 0.260 (DCC) 
• R-Value Work: 
  0.192 (Depositor), 0.210 (DCC) 
• R-Value Observed: 
  0.195 (Depositor) 

Starting Model: experimental

Literature

Three dimensional structure of human carbonic anhydrase XII in complex with benzenesulfonamide

Dvinskis, E., Leitans, J., Tars, K.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 121.24 kDa 
• Atom Count: 9,279 
• Modeled Residue Count: 1,040 
• Deposited Residue Count: 1,052 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 12	A, B, C, D	263	Homo sapiens	Mutation(s): 0  Gene Names: CA12 EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for O43570 (Homo sapiens) Explore O43570  Go to UniProtKB:  O43570
PHAROS:  O43570 GTEx:  ENSG00000074410

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
J95 (Subject of Investigation/LOI)	F [auth A], H [auth B], J [auth C], L [auth D]	~{N}-butyl-4-chloranyl-2-(cyclohexylamino)-5-sulfamoyl-benzamide C17 H26 Cl N3 O3 S WVNMCWQJUJCKNS-UHFFFAOYSA-N
ZN	E [auth A], G [auth B], I [auth C], K [auth D]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
J95	BindingDB:  6QNG	Kd: min: 7.7, max: 1.00e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.67 Å
• R-Value Free:  0.250 (Depositor), 0.260 (DCC) 
• R-Value Work:  0.192 (Depositor), 0.210 (DCC) 
• R-Value Observed: 0.195 (Depositor) 

Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 46.93	α = 82.09
b = 66.05	β = 84.41
c = 80.95	γ = 86.17

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2020-03-04 
Deposition Author(s): Dvinskis, E., Leitans, J., Tars, K.

Revision History  

• Version 1.0: 2020-03-04
  Type: Initial release
  
• Version 1.1: 2024-01-24
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.2: 2024-11-13
  Changes: Structure summary