3NJ9 | pdb_00003nj9

Crystal structure of carbonic anhydrase II in complex with a Nir inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3NJ9/pdb

• Classification: LYASE/LYASE INHIBITOR
• Organism(s): Homo sapiens
• Mutation(s): No 


• Deposited: 2010-06-17 Released: 2011-06-22 
• Deposition Author(s): Temperini, C., Cecchi, A.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free: 
  0.257 (Depositor), 0.207 (DCC) 
• R-Value Work: 
  0.200 (Depositor), 0.202 (DCC) 
• R-Value Observed: 
  0.202 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of carbonic anhydrase II in complex with a Nir inhibitor

Temperini, C., Cecchi, A.

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)

Macromolecule Content 

• Total Structure Weight: 30.33 kDa 
• Atom Count: 2,292 
• 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	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
TE2	D [auth A]	3-(4-sulfamoylphenyl)-N-[6-({(6Z)-2-[(2Z)-2-(1,3,3-trimethyl-1,3-dihydro-2H-indol-2-ylidene)ethyl]-6-[(2E)-2-(1,3,3-trimethyl-1,3-dihydro-2H-indol-2-ylidene)ethylidene]cyclohex-1-en-1-yl}amino)hexyl]propanamide C47 H61 N5 O3 S KNDSETYOKYYUHZ-OLEWYFQESA-N
HG	C [auth A]	MERCURY (II) ION Hg BQPIGGFYSBELGY-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.00 Å
• R-Value Free:  0.257 (Depositor), 0.207 (DCC) 
• R-Value Work:  0.200 (Depositor), 0.202 (DCC) 
• R-Value Observed: 0.202 (Depositor) 

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.07	α = 90
b = 41.54	β = 104.45
c = 72.39	γ = 90

Software Package:

Software Name	Purpose
CrysalisPro	data collection
AMoRE	phasing
REFMAC	refinement
CrysalisPro	data reduction
SCALEPACK	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-06-22 
Deposition Author(s): Temperini, C., Cecchi, A.

Revision History  

• Version 1.0: 2011-06-22
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-11-08
  Changes: Refinement description
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description