4E5O

Crystal structure of mouse thymidylate synthase in complex with dUMP

PDB DOI: https://doi.org/10.2210/pdb4E5O/pdb
Entry: 4E5O supersedes: 3IHH

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

Deposited: 2012-03-14 Released: 2012-04-18
Deposition Author(s): Dowiercial, A., Jarmula, A., Rypniewski, W., Sokolowska, M., Fraczyk, T., Ciesla, J., Rode, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.292
R-Value Work: 0.235
R-Value Observed: 0.236

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

Mouse thymidylate synthase does not show the inactive conformation, observed for the human enzyme

Dowiercial, A., Jarmula, A., Wilk, P., Rypniewski, W., Kowalska, M., Fraczyk, T., Ciesla, J., Rode, W.

(2016) Struct Chem

DOI: https://doi.org/10.1007/s11224-016-0840-8

Macromolecule Content

Total Structure Weight: 212.43 kDa
Atom Count: 15,512
Modelled Residue Count: 1,698
Deposited Residue Count: 1,842
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidylate synthase	A, B, C, D, E A, B, C, D, E, F	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% Identity50% Identity70% Identity90% Identity95% Identity100% 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 G [auth A] SDF format, chain H [auth B] SDF format, chain I [auth C] SDF format, chain M [auth D] SDF format, chain N [auth E] SDF format, chain O [auth F] SDF format, chain P [auth F] MOL2 format, chain G [auth A] MOL2 format, chain H [auth B] MOL2 format, chain I [auth C] MOL2 format, chain M [auth D] MOL2 format, chain N [auth E] MOL2 format, chain O [auth F] MOL2 format, chain P [auth F]	G [auth A] H [auth B] I [auth C] M [auth D] N [auth E] G [auth A], H [auth B], I [auth C], M [auth D], N [auth E], O [auth F], P [auth F]	2'-DEOXYURIDINE 5'-MONOPHOSPHATE C₉ H₁₃ N₂ O₈ P JSRLJPSBLDHEIO-SHYZEUOFSA-N		Interactions Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F] Interactions & Density Focus chain G [auth A] Focus chain H [auth B] Focus chain I [auth C] Focus chain M [auth D] Focus chain N [auth E] Focus chain O [auth F] Focus chain P [auth F]
BU1 Query on BU1 Download Ideal Coordinates CCD File SDF format, chain J [auth C] SDF format, chain K [auth C] SDF format, chain L [auth C] MOL2 format, chain J [auth C] MOL2 format, chain K [auth C] MOL2 format, chain L [auth C]	J [auth C], K [auth C], L [auth C]	1,4-BUTANEDIOL C₄ H₁₀ O₂ WERYXYBDKMZEQL-UHFFFAOYSA-N		Interactions Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C] Interactions & Density Focus chain J [auth C] Focus chain K [auth C] Focus chain L [auth C]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.70 Å
R-Value Free: 0.292
R-Value Work: 0.235
R-Value Observed: 0.236
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.35	α = 90
b = 88.54	β = 95.99
c = 136.76	γ = 90

Software Package:

Software Name	Purpose
SCALEPACK	data scaling
PHASER	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
DENZO	data reduction

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2012-04-18

Deposition Author(s):

This entry supersedes: 3IHH

Revision History (Full details and data files)

Version 1.0: 2012-04-18
Type: Initial release
Version 1.1: 2016-11-02
Changes: Database references
Version 1.2: 2018-03-07
Changes: Data collection
Version 1.3: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

4E5O

Crystal structure of mouse thymidylate synthase in complex with dUMP

Mouse thymidylate synthase does not show the inactive conformation, observed for the human enzyme

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)