3M98

Crystal structure of human carbonic anhydrase isozyme II with 5-(1H-benzimidazol-1-ylacetyl)-2-chlorobenzenesulfonamide

• PDB DOI:  https://doi.org/10.2210/pdb3M98/pdb

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


• Deposited: 2010-03-21 Released: 2011-03-02 
• Deposition Author(s): Grazulis, S., Manakova, E., Golovenko, D.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.184 
• R-Value Work: 0.135 
• R-Value Observed: 0.140 

Literature

Crystal structure of human carbonic anhydrase isozyme II with 5-(1H-benzimidazol-1-ylacetyl)-2-chlorobenzenesulfonamide

Capkauskaite, E., Baranauskiene, L., Grazulis, S., Manakova, E., Golovenko, D., Matulis, D.

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: 29.98 kDa 
• Atom Count: 2,348 
• Modelled 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  Gene Names: CA2 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

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
E02	C [auth A]	5-(1H-benzimidazol-1-ylacetyl)-2-chlorobenzenesulfonamide C15 H12 Cl N3 O3 S XXDZSNJTAQNIAQ-UHFFFAOYSA-N
MES	D [auth A]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
DMS	E [auth A]	DIMETHYL SULFOXIDE C2 H6 O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N
ZN	B [auth A]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
E02	BindingDB:  3M98	Kd: min: 1.5, max: 1600 (nM) from 7 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.184 
• R-Value Work: 0.135 
• R-Value Observed: 0.140 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.233	α = 90
b = 41.112	β = 104.05
c = 72.109	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling
PDB_EXTRACT	data extraction
MAR345	data collection

Structure Validation

Entry History 

Deposition Data

• Released Date: 2011-03-02 
Deposition Author(s): Grazulis, S., Manakova, E., Golovenko, D.

Revision History  

• Version 1.0: 2011-03-02
  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: 2023-09-06
  Changes: Data collection, Database references, Derived calculations, Refinement description