5P9S | pdb_00005p9s

humanized rat COMT in complex with 8-hydroxy-6-[3-methyl-5-(4-methylpiperazine-1-carbonyl)thiophen-2-yl]-3H-quinazolin-4-one

PDB DOI: https://doi.org/10.2210/pdb5P9S/pdb
Deposition Group: G_1002014 ExploreG_1002014

Classification: TRANSFERASE
Organism(s): Rattus norvegicus
Expression System: Escherichia coli BL21(DE3)
Mutation(s): Yes

Deposited: 2016-10-19 Released: 2017-11-22
Deposition Author(s): Ehler, A., Jakob-Roetne, R., Rudolph, M.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.258 (Depositor), 0.260 (DCC)
R-Value Work:
0.206 (Depositor), 0.200 (DCC)
R-Value Observed:
0.209 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Crystal Structure of a COMT complex

Lerner, C., Jakob-Roetne, R., Groebke-Zbinden, K., Buettelmann, B., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 25.49 kDa
Atom Count: 1,776
Modeled Residue Count: 214
Deposited Residue Count: 221
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A	221	Rattus norvegicus	Mutation(s): 2 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% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P22734
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7JK Query on 7JK 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]	6-[3-methyl-5-(4-methylpiperazin-1-yl)carbonyl-thiophen-2-yl]-8-oxidanyl-3~{H}-quinazolin-4-one C₁₉ H₂₀ N₄ O₃ S DNJWFDOPNCCIRY-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]
SAH Query on SAH 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]	S-ADENOSYL-L-HOMOCYSTEINE C₁₄ H₂₀ N₆ O₅ S ZJUKTBDSGOFHSH-WFMPWKQPSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
MG Query on MG 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]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.258 (Depositor), 0.260 (DCC)
R-Value Work: 0.206 (Depositor), 0.200 (DCC)
R-Value Observed: 0.209 (Depositor)

Space Group: P 3₂ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.517	α = 90
b = 50.517	β = 90
c = 168.856	γ = 120

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-11-22

Deposition Author(s):

Jakob-Roetne, R.

Revision History (Full details and data files)

Version 1.0: 2017-11-22
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

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.