5LQU | pdb_00005lqu

Crystal Structure of COMT in complex with N-[(E)-3-[(2R,3S,4R,5R)-5-[6-(ethylamino)purin-9-yl]-3,4-dihydroxyoxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide

• PDB DOI: https://doi.org/10.2210/pdb5LQU/pdb

• Classification: TRANSFERASE
• Organism(s): Rattus norvegicus
• Expression System: Escherichia coli BL21(DE3)
• Mutation(s): No 


• Deposited: 2016-08-17 Released: 2016-10-05 
• Deposition Author(s): Ehler, A., Lerner, C., Ellermann, M., Rudolph, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free: 
  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.163 (Depositor), 0.170 (DCC) 
• R-Value Observed: 
  0.165 (Depositor) 

Starting Model: other

Literature

Crystal Structure of COMT in complex with N-[(E)-3-[(2R,3S,4R,5R)-5-[6-(ethylamino)purin-9-yl]-3,4-dihydroxyoxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide

Lerner, C., Ellermann, M., Rudolph, M.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 51.01 kDa 
• Atom Count: 3,922 
• Modeled Residue Count: 427 
• Deposited Residue Count: 442 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A, B	221	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
619	C [auth A], H [auth B]	N-[(E)-3-[(2R,3S,4R,5R)-5-(6-ethylaminopurin-9-yl)-3,4-dihydroxy-oxolan-2-yl]prop-2-enyl]-5-(4-fluorophenyl)-2,3-dihydroxy-benzamide C27 H27 F N6 O6 NOCNCHHJBSJZFZ-CJLJSIFTSA-N
BTB	G [auth A]	2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL C8 H19 N O5 OWMVSZAMULFTJU-UHFFFAOYSA-N
CL	E [auth A], F [auth A], J [auth B]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	D [auth A], I [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.80 Å
• R-Value Free:  0.205 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.163 (Depositor), 0.170 (DCC) 
• R-Value Observed: 0.165 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 56.154	α = 90
b = 61.571	β = 90
c = 130.941	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
PDB_EXTRACT	data extraction
REFMAC	refinement
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2016-10-05 
Deposition Author(s): Ehler, A., Lerner, C., Ellermann, M., Rudolph, M.G.

Revision History  

• Version 1.0: 2016-10-05
  Type: Initial release
  
• Version 1.1: 2024-05-01
  Changes: Data collection, Database references, Derived calculations, Refinement description