3A7D | pdb_00003a7d

Crystal Structures of rat Catechol-O-Methyltransferase complexed with new bi-substrate type inhibitor

• PDB DOI: https://doi.org/10.2210/pdb3A7D/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-09-26 Released: 2010-09-15 
• Deposition Author(s): Tsuji, E.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free: 
  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work: 
  0.159 (Depositor), 0.166 (DCC) 
• R-Value Observed: 
  0.166 (Depositor) 

Starting Model: experimental

Literature

Hit to Lead: Comprehensive Strategy of de novo Scaffold Generation by FBDD. Part 2: Ligand Fishing using Mass Spectrometry by Detection of Ligand-Protein Non-Covalent Complex after Matrix Click Chemistry

Muranaka, H., Nakatsu, M., Tsuji, E., Okazaki, K.

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: 25.66 kDa 
• Atom Count: 1,818 
• Modeled Residue Count: 214 
• Deposited Residue Count: 223 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A	223	Rattus norvegicus	Mutation(s): 0  Gene Names: Comt EC: 2.1.1.6
UniProt
Find proteins for P22734 (Rattus norvegicus) Explore P22734  Go to UniProtKB:  P22734

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FBN	E [auth A]	5'-deoxy-5'-[4-({[(2,3-dihydroxy-5-nitrophenyl)carbonyl]amino}methyl)-1H-1,2,3-triazol-1-yl]adenosine C20 H20 N10 O8 KWTYQIOJSHGBKG-VXHCAWKWSA-N
SO4	C [auth A], D [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.40 Å
• R-Value Free:  0.225 (Depositor), 0.220 (DCC) 
• R-Value Work:  0.159 (Depositor), 0.166 (DCC) 
• R-Value Observed: 0.166 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.075	α = 90
b = 58.082	β = 90
c = 79.198	γ = 90

Software Package:

Software Name	Purpose
BSS	data collection
AMoRE	phasing
REFMAC	refinement
MOSFLM	data reduction
SCALA	data scaling

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-09-15 
Deposition Author(s): Tsuji, E.

Revision History  

• Version 1.0: 2010-09-15
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary