4EIN

Crystal structure of mouse thymidylate synthase in binary complex with a substrate analogue and strong inhibitor, N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate

PDB DOI: https://doi.org/10.2210/pdb4EIN/pdb

Classification: Transferase/Transferase Inhibitor
Organism(s): Mus musculus
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2012-04-05 Released: 2013-04-10
Deposition Author(s): Dowiercial, A., Jarmula, A., Rypniewski, W.R., Wilk, P., Kierdaszuk, B., Rode, W.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.255
R-Value Work: 0.206
R-Value Observed: 0.208

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Crystal structures of complexes of mouse thymidylate synthase crystallized with N4-OH-dCMP alone or in the presence of N5,10-methylenetetrahydrofolate

Dowiercial, A., Jarmula, A., Rypniewski, W.R., Wilk, P., Kierdaszuk, B., Rode, W.

(2013) Pteridines

Macromolecule Content

Total Structure Weight: 70.74 kDa
Atom Count: 5,462
Modelled Residue Count: 569
Deposited Residue Count: 614
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	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
NOH Query on NOH Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	2'-deoxy-N-hydroxycytidine 5'-(dihydrogen phosphate) C₉ H₁₄ N₃ O₈ P YKOWBJJOJNGCAD-SHYZEUOFSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain E [auth B] MOL2 format, chain E [auth B] mmCIF format, chain E [auth B]	E [auth B]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain E [auth B] Interactions & Density Focus chain E [auth B]

Binding Affinity Annotations
ID	Source	Binding Affinity
NOH	BindingDB: 4EIN	Kd: 1000 (nM) from 1 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.75 Å
R-Value Free: 0.255
R-Value Work: 0.206
R-Value Observed: 0.208
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 160.023	α = 90
b = 87.956	β = 96.44
c = 68.668	γ = 90

Software Package:

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

Structure Validation

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Entry History

Deposition Data

Released Date: 2013-04-10

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-04-10
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description

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4EIN

Crystal structure of mouse thymidylate synthase in binary complex with a substrate analogue and strong inhibitor, N(4)-hydroxy-2'-deoxycytidine-5'-monophosphate

Crystal structures of complexes of mouse thymidylate synthase crystallized with N4-OH-dCMP alone or in the presence of N5,10-methylenetetrahydrofolate

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)