4EAD

Thymidine phosphorylase from E.coli with 3'-azido-2'-fluoro-dideoxyuridine

PDB DOI: https://doi.org/10.2210/pdb4EAD/pdb

Classification: Transferase/Transferase inhibitor
Organism(s): Escherichia coli K-12
Expression System: Escherichia coli BL21(DE3)
Mutation(s): No

Deposited: 2012-03-22 Released: 2013-03-27
Deposition Author(s): Timofeev, V.I., Abramchik, Y.A., Esipov, R.S., Kuranova, I.P.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.192
R-Value Work: 0.145
R-Value Observed: 0.147

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

Thymidine phosphorylase from E.coli with 3'-azido-2'-fluoro-dideoxyuridine

Timofeev, V.I., Abramchik, Y.A., Esipov, R.S., Kuranova, I.P.

To be published.

Macromolecule Content

Total Structure Weight: 48.46 kDa
Atom Count: 3,984
Modelled Residue Count: 440
Deposited Residue Count: 440
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Thymidine phosphorylase	A	440	Escherichia coli K-12	Mutation(s): 0 Gene Names: b4382, deoA, JW4345, tpp, ttg EC: 2.4.2.4
UniProt
Find proteins for P07650 (Escherichia coli (strain K12)) Explore P07650 Go to UniProtKB: P07650
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P07650
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
0NP Query on 0NP 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',3'-dideoxy-2'-fluoro-3'-triaza-1,2-dien-2-ium-1-yluridine C₉ H₁₁ F N₅ O₄ YRIDFNZYEULFDH-XVFCMESISA-O		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth A] SDF format, chain E [auth A] SDF format, chain G [auth A] SDF format, chain K [auth A] SDF format, chain L [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A] MOL2 format, chain E [auth A] MOL2 format, chain G [auth A] MOL2 format, chain K [auth A] MOL2 format, chain L [auth A] mmCIF format, chain C [auth A] mmCIF format, chain D [auth A] mmCIF format, chain E [auth A] mmCIF format, chain G [auth A] mmCIF format, chain K [auth A] mmCIF format, chain L [auth A]	C [auth A] D [auth A] E [auth A] G [auth A] K [auth A] C [auth A], D [auth A], E [auth A], G [auth A], K [auth A], L [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain K [auth A] Focus chain L [auth A] Interactions & Density Focus chain C [auth A] Focus chain D [auth A] Focus chain E [auth A] Focus chain G [auth A] Focus chain K [auth A] Focus chain L [auth A]
GOL Query on GOL Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A]	F [auth A], H [auth A], I [auth A], J [auth A]	GLYCEROL C₃ H₈ O₃ PEDCQBHIVMGVHV-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.50 Å
R-Value Free: 0.192
R-Value Work: 0.145
R-Value Observed: 0.147
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 129.862	α = 90
b = 129.862	β = 90
c = 67.656	γ = 90

Software Package:

Software Name	Purpose
HKL-2000	data collection
PHASER	phasing
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2013-03-27

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2013-03-27
Type: Initial release
Version 1.1: 2023-09-13
Changes: Data collection, Database references, Derived calculations, Refinement description