5ZY6 | pdb_00005zy6

catechol methyltransferase spCOMT

PDB DOI: https://doi.org/10.2210/pdb5ZY6/pdb

Classification: TRANSFERASE
Organism(s): Schizosaccharomyces pombe 972h-
Expression System: Escherichia coli K-12
Mutation(s): No

Deposited: 2018-05-22 Released: 2019-05-22
Deposition Author(s): Wang, Q., Xu, L.
Funding Organization(s): National Natural Science Foundation of China

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free:
0.234 (Depositor), 0.230 (DCC)
R-Value Work:
0.185 (Depositor), 0.190 (DCC)
R-Value Observed:
0.188 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

structural insight into spCOMT

Wang, Q.

To be published.

Macromolecule Content

Total Structure Weight: 63.62 kDa
Atom Count: 4,226
Modeled Residue Count: 485
Deposited Residue Count: 548
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Probable catechol O-methyltransferase 1	A, B	274	Schizosaccharomyces pombe 972h-	Mutation(s): 0 EC: 2.1.1.6
UniProt
Find proteins for O42898 (Schizosaccharomyces pombe (strain 972 / ATCC 24843)) Explore O42898 Go to UniProtKB: O42898
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O42898
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SAM Query on SAM Download Ideal Coordinates CCD File SDF format, chain D [auth B] SDF format, chain C [auth A] MOL2 format, chain D [auth B] MOL2 format, chain C [auth A] mmCIF format, chain D [auth B] mmCIF format, chain C [auth A]	C [auth A], D [auth B]	S-ADENOSYLMETHIONINE C₁₅ H₂₂ N₆ O₅ S MEFKEPWMEQBLKI-FCKMPRQPSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.10 Å
R-Value Free: 0.234 (Depositor), 0.230 (DCC)
R-Value Work: 0.185 (Depositor), 0.190 (DCC)
R-Value Observed: 0.188 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.265	α = 90
b = 78.858	β = 90
c = 102.781	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
HKL-2000	data reduction
HKL-2000	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2019-05-22

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation of China	China	U1732114, 31770788, 31770895

Revision History (Full details and data files)

Version 1.0: 2019-05-22
Type: Initial release
Version 1.1: 2023-11-22
Changes: Data collection, Database references, 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.