5P9A | pdb_00005p9a

rat catechol O-methyltransferase in complex with N-[2-[2-(6-aminopurin-9-yl)ethoxy]ethyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide at 1.91A

PDB DOI: https://doi.org/10.2210/pdb5P9A/pdb
Deposition Group: G_1002010 | Explore G_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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free:
0.284 (Depositor), 0.242 (DCC)
R-Value Work:
0.219 (Depositor), 0.191 (DCC)
R-Value Observed:
0.222 (Depositor)

Starting Model: other
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Ligand Structure Quality Assessment

This is version 1.3 of the entry. See complete history.

Literature

Crystal Structure of a COMT complex

Lerner, C., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 25.44 kDa
Atom Count: 1,996
Modeled Residue Count: 213
Deposited Residue Count: 221
Unique protein chains: 1

Macromolecules

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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
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P22734
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
77N Query on 77N Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	N-[2-[2-(6-aminopurin-9-yl)ethoxy]ethyl]-5-(4-fluorophenyl)-2,3-dihydroxybenzamide C₂₂ H₂₁ F N₆ O₄ MBDKBZKJWMEJRT-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
D1D Query on D1D Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	(4S,5S)-1,2-DITHIANE-4,5-DIOL C₄ H₈ O₂ S₂ YPGMOWHXEQDBBV-QWWZWVQMSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
K Query on K Download:Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
MG Query on MG Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.91 Å
R-Value Free: 0.284 (Depositor), 0.242 (DCC)
R-Value Work: 0.219 (Depositor), 0.191 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 49.945	α = 90
b = 53.653	β = 90
c = 80.638	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2017-08-30

Deposition Author(s):

Revision History (Full details and data files)

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, Structure summary
Version 1.3: 2024-04-03
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.