5K01 | pdb_00005k01

Crystal Structure of COMT in complex with 2,7-dimethyl-3-(1H-pyrazol-3-yl)imidazo[1,2-a]pyridine

PDB DOI: https://doi.org/10.2210/pdb5K01/pdb

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

Deposited: 2016-05-17 Released: 2016-09-07
Deposition Author(s): Ehler, A., Rodriguez-Sarmiento, R.M., Rudolph, M.G.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.38 Å
R-Value Free:
0.176 (Depositor), 0.179 (DCC)
R-Value Work:
0.134 (Depositor), 0.137 (DCC)
R-Value Observed:
0.137 (Depositor)

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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

Crystal Structure of COMT

Ehler, A., Rodriguez-Sarmiento, R.M., Rudolph, M.G.

To be published.

Macromolecule Content

Total Structure Weight: 24.24 kDa
Atom Count: 2,057
Modeled Residue Count: 214
Deposited Residue Count: 214
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Catechol O-methyltransferase	A	214	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 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
6OW Query on 6OW 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]	2,7-dimethyl-3-(1H-pyrazol-5-yl)imidazo[1,2-a]pyridine C₁₂ H₁₂ N₄ ZNRUSTFXUSPVPD-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
K Query on K 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]	POTASSIUM ION K NPYPAHLBTDXSSS-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: 1.38 Å
R-Value Free: 0.176 (Depositor), 0.179 (DCC)
R-Value Work: 0.134 (Depositor), 0.137 (DCC)
R-Value Observed: 0.137 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 33.789	α = 90
b = 59.788	β = 90
c = 108.093	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2016-09-07

Deposition Author(s):

Rodriguez-Sarmiento, R.M.

Revision History (Full details and data files)

Version 1.0: 2016-09-07
Type: Initial release
Version 1.1: 2019-06-12
Changes: Data collection, Database references, Structure summary
Version 1.2: 2024-05-08
Changes: Data collection, Database references

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