3M1J

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

Structural Biology Knowledgebase: 3M1J SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.193

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 3M1J

Classification: LYASE

Total Structure Weight: 29924.67

Macromolecule Entities
Molecule Chains Length Organism Details
Carbonic anhydrase 2 A 260 Homo sapiens EC#: 4.2.1.1 IUBMB
Gene Name(s): CA2 Gene View
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 5 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
MBO
Query on MBO

A MERCURIBENZOIC ACID
C7 H5 Hg O2
FVFZSVRSDNUCGG-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
RU
Query on RU

A RUTHENIUM ION
Ru
BPEVHDGLPIIAGH-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
DMS
Query on DMS

A DIMETHYL SULFOXIDE
C2 H6 O S
IAZDPXIOMUYVGZ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
IMD
Query on IMD

A IMIDAZOLE
C3 H5 N2
RAXXELZNTBOGNW-UHFFFAOYSA-O
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
ZN
Query on ZN

A ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
External Ligand Annotations
ID Binding Affinity (Sequence Identity %)
IMD N/A in BindingDB
N/A in BindingMoad
IC50: 15000 nM  PDBbind

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.8 Å
  • R-Value Free: 0.235
  • R-Value Work: 0.193
  • Space Group: P 1 21 1
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 42.10 α = 90.00
b = 41.55 β = 104.51
c = 72.29 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

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

Revision History

  • 2011-07-13
    Type: Version format compliance | Details: compliance with PDB Exchange Dictionary V4