3A7E | pdb_00003a7e

Crystal structure of human COMT complexed with SAM and 3,5-dinitrocatechol

• PDB DOI: https://doi.org/10.2210/pdb3A7E/pdb

• Classification: TRANSFERASE
• Organism(s): Homo sapiens
• 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: 2.80 Å
• R-Value Free: 
  0.298 (Depositor), 0.298 (DCC) 
• R-Value Work: 
  0.218 (Depositor), 0.223 (DCC) 
• R-Value Observed: 
  0.226 (Depositor) 

Starting Model: experimental

Literature

Hit to Lead: Comprehensive Strategy of de novo Scaffold Generation by FBDD. Part 1: In silico Fragments Linking and Verification of Spatial Proximity using Inter Ligand NOE Approachs

Nonaka, Y., Momose, T., Ozawa, T., Ozawa, M., Nakatsu, M., Tsuji, E., Okazaki, K., Takase, Y., Kiyotani, T.

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: 24.65 kDa 
• Atom Count: 1,748 
• Modeled Residue Count: 212 
• Deposited Residue Count: 216 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A	216	Homo sapiens	Mutation(s): 0  Gene Names: COMT EC: 2.1.1.6
UniProt & NIH Common Fund Data Resources
Find proteins for P21964 (Homo sapiens) Explore P21964  Go to UniProtKB:  P21964
PHAROS:  P21964 GTEx:  ENSG00000093010

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SAM	C [auth A]	S-ADENOSYLMETHIONINE C15 H22 N6 O5 S MEFKEPWMEQBLKI-FCKMPRQPSA-N
DNC	D [auth A]	3,5-DINITROCATECHOL C6 H4 N2 O6 VDCDWNDTNSWDFJ-UHFFFAOYSA-N
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.80 Å
• R-Value Free:  0.298 (Depositor), 0.298 (DCC) 
• R-Value Work:  0.218 (Depositor), 0.223 (DCC) 
• R-Value Observed: 0.226 (Depositor) 

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.909	α = 90
b = 50.909	β = 90
c = 168.186	γ = 120

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