5LLA | pdb_00005lla

Crystal structure of human carbonic anhydrase isozyme XIII with 4-(1H-benzimidazol-1-ylacetyl)-2-chlorobenzenesulfonamide

• PDB DOI: https://doi.org/10.2210/pdb5LLA/pdb

• Classification: LYASE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-07-27 Released: 2017-08-16 
• Deposition Author(s): Smirnov, A., Manakova, E., Grazulis, S.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 
  0.212 (Depositor), 0.201 (DCC) 
• R-Value Work: 
  0.179 (Depositor) 
• R-Value Observed: 
  0.182 (Depositor) 

Starting Model: experimental

Literature

Combinatorial Design of Isoform-Selective N-Alkylated Benzimidazole-Based Inhibitors of Carbonic Anhydrases

Capkauskaite, E., Linkuviene, V., Smirnov, A., Milinaviciute, G., Timm, D., Kasiliauskaite, A., Manakova, E., Grazulis, S., Matulis, D.

(2017) ChemistrySelect 

• DOI: https://doi.org/10.1002/slct.201700531

Biological Assembly 1  

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

Biological assembly 1 assigned by authors.

Biological Assembly 2  

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

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 60.57 kDa 
• Atom Count: 4,853 
• Modeled Residue Count: 516 
• Deposited Residue Count: 526 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Carbonic anhydrase 13	A [auth B], B [auth A]	263	Homo sapiens	Mutation(s): 0  Gene Names: CA13 EC: 4.2.1.1
UniProt & NIH Common Fund Data Resources
Find proteins for Q8N1Q1 (Homo sapiens) Explore Q8N1Q1  Go to UniProtKB:  Q8N1Q1
PHAROS:  Q8N1Q1 GTEx:  ENSG00000185015

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
6YQ	D [auth B], H [auth A]	4-[2-(benzimidazol-1-yl)ethanoyl]-2-chloranyl-benzenesulfonamide C15 H12 Cl N3 O3 S SWJLGRBJIPSPCI-UHFFFAOYSA-N
CIT	E [auth B], I [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ZN	C [auth B], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N
EDO	F [auth B], J [auth A]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
6YQ	BindingDB:  5LLA	Kd: min: 0.19, max: 19 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free:  0.212 (Depositor), 0.201 (DCC) 
• R-Value Work:  0.179 (Depositor) 
• R-Value Observed: 0.182 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.023	α = 90
b = 57.276	β = 90
c = 159.284	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALA	data scaling
PDB_EXTRACT	data extraction
XDS	data reduction
MOLREP	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-16 
Deposition Author(s): Smirnov, A., Manakova, E., Grazulis, S.

Revision History  

• Version 1.0: 2017-08-16
  Type: Initial release
  
• Version 1.1: 2017-11-29
  Changes: Database references
• Version 1.2: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description