Macromolecule Content

Total Structure Weight: 29.92 kDa
Atom Count: 2290
Residue Count: 257
Unique protein chains: 1

3M1J

The crystal structure of a NAMI A-Carbonic Anhydrase II adduct discloses the mode of action of this novel anticancer metallodrug

DOI: 10.2210/pdb3M1J/pdb

Classification: LYASE
Organism(s): Homo sapiens
Mutation(s): No

Deposited: 2010-03-05 Released: 2011-01-19
Deposition Author(s): Temperini, C., Messori, L.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.235
R-Value Work: 0.193
R-Value Observed: 0.195

wwPDB Validation3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

The x-ray structure of the adduct between NAMI-A and carbonic anhydrase provides insights into the reactivity of this metallodrug with proteins

Casini, A., Temperini, C., Gabbiani, C., Supuran, C.T., Messori, L.

(2010) ChemMedChem 5: 1989-1994

Macromolecules

Find similar proteins by: Sequence | Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details
Carbonic anhydrase 2	A	260	Homo sapiens	Mutation(s): 0 Gene Names: CA2 EC: 4.2.1.1
Find proteins for P00918 (Homo sapiens) Go to UniProtKB: P00918
NIH Common Fund Data Resources
PHAROS P00918 GTEx ENSG00000104267
Protein Feature View Full Protein Feature View for P00918

Small Molecules

Ligands 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
MBO Query on MBO Download CCD File	A	MERCURIBENZOIC ACID C₇ H₅ Hg O₂ FVFZSVRSDNUCGG-UHFFFAOYSA-N		Ligand Interaction
RU Query on RU Download CCD File	A	RUTHENIUM ION Ru BPEVHDGLPIIAGH-UHFFFAOYSA-N		Ligand Interaction
DMS Query on DMS Download CCD File	A	DIMETHYL SULFOXIDE C₂ H₆ O S IAZDPXIOMUYVGZ-UHFFFAOYSA-N		Ligand Interaction
IMD Query on IMD Download CCD File	A	IMIDAZOLE C₃ H₅ N₂ RAXXELZNTBOGNW-UHFFFAOYSA-O		Ligand Interaction
ZN Query on ZN Download CCD File	A	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Ligand Interaction

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
IMD	IC50 : 15000 nM PDBBind

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.80 Å
R-Value Free: 0.235
R-Value Work: 0.193
R-Value Observed: 0.195
Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 42.1	α = 90
b = 41.55	β = 104.51
c = 72.29	γ = 90

Software Package:

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

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Deposited Date: 2010-03-05
Released Date: 2011-01-19

Deposition Author(s):

Revision History

Version 1.0: 2011-01-19
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2017-11-08
Changes: Refinement description

RCSB PDB is funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.