6Y08 | pdb_00006y08

Mouse thymidylate synthase cocrystallized with dUMP and soaked in sulfamethoxazole

PDB DOI: https://doi.org/10.2210/pdb6Y08/pdb

Classification: TRANSFERASE
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2020-02-06 Released: 2021-02-17
Deposition Author(s): Maj, P., Jarmula, A., Wilk, P., Weiss, M.S., Rode, W.
Funding Organization(s): Polish National Science Centre

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free:
0.250 (Depositor), 0.254 (DCC)
R-Value Work:
0.210 (Depositor), 0.214 (DCC)
R-Value Observed:
0.212 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

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Ligand Structure Quality Assessment

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

Literature

Mouse thymidylate synthase cocrystallized with dUMP and soaked in sulfamethoxazole

Maj, P., Jarmula, A., Wilk, P., Weiss, M.S., Rode, W.

To be published.

Macromolecule Content

Total Structure Weight: 71.12 kDa
Atom Count: 4,630
Modeled Residue Count: 557
Deposited Residue Count: 614
Unique protein chains: 1

Macromolecules

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Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B	307	Mus musculus	Mutation(s): 0 Gene Names: Tyms EC: 2.1.1.45
UniProt
Find proteins for P07607 (Mus musculus) Explore P07607 Go to UniProtKB: P07607
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P07607
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
UMP Query on UMP Download:Ideal Coordinates CCD File SDF format, chain E [auth B] SDF format, chain C [auth A] MOL2 format, chain E [auth B] MOL2 format, chain C [auth A] mmCIF format, chain E [auth B] mmCIF format, chain C [auth A]	C [auth A], E [auth B]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain C [auth A] Focus chain E [auth B] Interactions & Density Focus chain C [auth A] Focus chain E [auth B]
08D (Subject of Investigation/LOI) Query on 08D Download:Ideal Coordinates CCD File SDF format, chain F [auth B] SDF format, chain D [auth A] MOL2 format, chain F [auth B] MOL2 format, chain D [auth A] mmCIF format, chain F [auth B] mmCIF format, chain D [auth A]	D [auth A], F [auth B]	Sulfamethoxazole C₁₀ H₁₁ N₃ O₃ S JLKIGFTWXXRPMT-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain F [auth B] Interactions & Density Focus chain D [auth A] Focus chain F [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.30 Å
R-Value Free: 0.250 (Depositor), 0.254 (DCC)
R-Value Work: 0.210 (Depositor), 0.214 (DCC)
R-Value Observed: 0.212 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.545	α = 90
b = 88.057	β = 96.15
c = 68.262	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
DENZO	data reduction
SCALEPACK	data scaling
PHASES	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2021-02-17

Deposition Author(s):

Funding Organization	Location	Grant Number
Polish National Science Centre	Poland	2016/21/B/NZ1/00288

Revision History (Full details and data files)

Version 1.0: 2021-02-17
Type: Initial release
Version 1.1: 2024-01-24
Changes: Data collection, Database references, 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.