5LLN | pdb_00005lln

Crystal structure of human carbonic anhydrase isozyme XIII with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide

• PDB DOI: https://doi.org/10.2210/pdb5LLN/pdb

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


• Deposited: 2016-07-28 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: 1.60 Å
• R-Value Free: 
  0.206 (Depositor), 0.203 (DCC) 
• R-Value Work: 
  0.168 (Depositor), 0.167 (DCC) 
• R-Value Observed: 
  0.172 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of human carbonic anhydrase isozyme XIII with 2,3,5,6-Tetrafluoro-4-(propylthio)benzenesulfonamide

Smirnov, A., Manakova, E., Grazulis, S., Matulis, D.

To be published.

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: 60.54 kDa 
• Atom Count: 4,908 
• Modeled Residue Count: 517 
• 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 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
3TV	F [auth B], I [auth A]	2,3,5,6-tetrafluoro-4-(propylsulfanyl)benzenesulfonamide C9 H9 F4 N O2 S2 LKPIFWBRFVJTMY-UHFFFAOYSA-N
CIT	D [auth B], E [auth B], H [auth A]	CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N
ZN	C [auth B], G [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
3TV	BindingDB:  5LLN	Kd: min: 0.53, max: 1.7 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.60 Å
• R-Value Free:  0.206 (Depositor), 0.203 (DCC) 
• R-Value Work:  0.168 (Depositor), 0.167 (DCC) 
• R-Value Observed: 0.172 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.52	α = 90
b = 57.334	β = 90
c = 159.708	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: 2024-01-10
  Changes: Data collection, Database references, Derived calculations, Refinement description