5P96 | pdb_00005p96

rat catechol O-methyltransferase in complex with N-[5-(2-aminopurin-9-yl)pentyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide at 1.40A

• PDB DOI: https://doi.org/10.2210/pdb5P96/pdb
• Deposition Group: G_1002010 ExploreG_1002010

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


• Deposited: 2016-08-30 Released: 2017-08-30 
• Deposition Author(s): Ehler, A., Lerner, C., Rudolph, M.G.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free: 
  0.147 (Depositor), 0.140 (DCC) 
• R-Value Work: 
  0.111 (Depositor), 0.110 (DCC) 
• R-Value Observed: 
  0.113 (Depositor) 

Starting Model: other

Literature

Crystal Structure of a COMT complex

Lerner, C., Rudolph, M.G.

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: 25.87 kDa 
• Atom Count: 2,077 
• Modeled Residue Count: 213 
• Deposited Residue Count: 221 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A	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 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
77H	C [auth A]	N-[5-(2-aminopurin-9-yl)pentyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide C23 H23 F N6 O3 KUZQYEZWVYHXLQ-UHFFFAOYSA-N
NHE	E [auth A]	2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID C8 H17 N O3 S MKWKNSIESPFAQN-UHFFFAOYSA-N
D1D	D [auth A]	(4S,5S)-1,2-DITHIANE-4,5-DIOL C4 H8 O2 S2 YPGMOWHXEQDBBV-QWWZWVQMSA-N
SO4	H [auth A], I [auth A]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
CL	F [auth A], G [auth A]	CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M
MG	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.40 Å
• R-Value Free:  0.147 (Depositor), 0.140 (DCC) 
• R-Value Work:  0.111 (Depositor), 0.110 (DCC) 
• R-Value Observed: 0.113 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.87	α = 90
b = 54.267	β = 90
c = 81.075	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-08-30 
Deposition Author(s): Ehler, A., Lerner, C., Rudolph, M.G.

Revision History  

• Version 1.0: 2017-08-30
  Type: Initial release
  
• Version 1.1: 2018-02-21
  Changes: Structure summary
• Version 1.2: 2021-11-17
  Changes: Database references, Derived calculations, Structure summary
• Version 1.3: 2024-04-03
  Changes: Data collection, Refinement description