5P8W | pdb_00005p8w

Crystal Structure of COMT in complex with [5-(2,4-dimethyl-1,3-thiazol-5-yl)-1H-pyrazol-3-yl]methanamine

PDB DOI: https://doi.org/10.2210/pdb5P8W/pdb
Deposition Group: G_1002007 ExploreG_1002007

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

Deposited: 2016-08-25 Released: 2016-09-07
Deposition Author(s): Ehler, A., Lerner, C., Rudolph, M.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free:
0.204 (Depositor), 0.210 (DCC)
R-Value Work:
0.168 (Depositor), 0.170 (DCC)
R-Value Observed:
0.170 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.5 of the entry. See complete history.

Literature

Crystal Structure of COMT complex

Lerner, C., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 75.42 kDa
Atom Count: 5,495
Modeled Residue Count: 640
Deposited Residue Count: 663
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, B, C	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 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
O01 Query on O01 Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain J [auth B] SDF format, chain O [auth C] MOL2 format, chain E [auth A] MOL2 format, chain J [auth B] MOL2 format, chain O [auth C] mmCIF format, chain E [auth A] mmCIF format, chain J [auth B] mmCIF format, chain O [auth C]	E [auth A], J [auth B], O [auth C]	[5-(2,4-dimethyl-1,3-thiazol-5-yl)-1H-pyrazol-3-yl]methanamine C₉ H₁₂ N₄ S IPDYKGULJOZYNW-UHFFFAOYSA-N		Interactions Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C] Interactions & Density Focus chain E [auth A] Focus chain J [auth B] Focus chain O [auth C]
DTT Query on DTT Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain I [auth B] SDF format, chain N [auth C] MOL2 format, chain D [auth A] MOL2 format, chain I [auth B] MOL2 format, chain N [auth C] mmCIF format, chain D [auth A] mmCIF format, chain I [auth B] mmCIF format, chain N [auth C]	D [auth A], I [auth B], N [auth C]	2,3-DIHYDROXY-1,4-DITHIOBUTANE C₄ H₁₀ O₂ S₂ VHJLVAABSRFDPM-IMJSIDKUSA-N		Interactions Focus chain D [auth A] Focus chain I [auth B] Focus chain N [auth C] Interactions & Density Focus chain D [auth A] Focus chain I [auth B] Focus chain N [auth C]
FMT Query on FMT Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain K [auth B] SDF format, chain P [auth C] MOL2 format, chain F [auth A] MOL2 format, chain K [auth B] MOL2 format, chain P [auth C] mmCIF format, chain F [auth A] mmCIF format, chain K [auth B] mmCIF format, chain P [auth C]	F [auth A], K [auth B], P [auth C]	FORMIC ACID C H₂ O₂ BDAGIHXWWSANSR-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C] Interactions & Density Focus chain F [auth A] Focus chain K [auth B] Focus chain P [auth C]
NA Query on NA Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain H [auth A] SDF format, chain L [auth B] SDF format, chain M [auth B] SDF format, chain Q [auth C] MOL2 format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain L [auth B] MOL2 format, chain M [auth B] MOL2 format, chain Q [auth C] mmCIF format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain L [auth B] mmCIF format, chain M [auth B] mmCIF format, chain Q [auth C]	G [auth A], H [auth A], L [auth B], M [auth B], Q [auth C]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C] Interactions & Density Focus chain G [auth A] Focus chain H [auth A] Focus chain L [auth B] Focus chain M [auth B] Focus chain Q [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.03 Å
R-Value Free: 0.204 (Depositor), 0.210 (DCC)
R-Value Work: 0.168 (Depositor), 0.170 (DCC)
R-Value Observed: 0.170 (Depositor)

Space Group: C 2 2 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 94.931	α = 90
b = 176.379	β = 90
c = 119.6	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2016-09-07

Deposition Author(s):

Ehler, A.

Lerner, C.

Rudolph, M.G.

Revision History (Full details and data files)

Version 1.0: 2016-09-07
Type: Initial release
Version 1.1: 2018-02-21
Changes: Derived calculations, 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
Version 1.4: 2024-05-01
Changes: Derived calculations
Version 1.5: 2024-10-30
Changes: Structure summary