Download MendeleyX-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with cytidine and sulphate
Balaev, V.V., Lashkov, A.A., Gabdulkhakov, A.G., Betzel, C., Mikhailov, A.M.To be published.
5EY3
X-ray structure of the thymidine phosphorylase from Salmonella typhimurium in complex with cytidine and sulphate
- PDB DOI: https://doi.org/10.2210/pdb5EY3/pdb
- Classification: TRANSFERASE
- Organism(s): Salmonella enterica subsp. enterica serovar Typhimurium str. LT2
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-11-24 Released: 2016-12-07
- Funding Organization(s): Russian Foundation for Basic Research
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.91 Å
- R-Value Free: 0.238
- R-Value Work: 0.200
- R-Value Observed: 0.202
This is version 1.2 of the entry. See complete history.
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| Thymidine phosphorylase | 442 | Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 | Mutation(s): 0 Gene Names: deoA, STM4568 EC: 2.4.2.4 |  | |
UniProt | |||||
Find proteins for Q7CP66 (Salmonella typhimurium (strain LT2 / SGSC1412 / ATCC 700720)) Explore Q7CP66 Go to UniProtKB: Q7CP66 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q7CP66 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CTN Query on CTN | O [auth B] | 4-AMINO-1-BETA-D-RIBOFURANOSYL-2(1H)-PYRIMIDINONE C9 H13 N3 O5 UHDGCWIWMRVCDJ-XVFCMESISA-N |  | ||
| SO4 Query on SO4 | C [auth A] D [auth A] E [auth A] F [auth A] G [auth A] | SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L |  | ||
| GOL Query on GOL | H [auth A], N [auth B] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| EDO Query on EDO | I [auth A] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.91 Å
- R-Value Free: 0.238
- R-Value Work: 0.200
- R-Value Observed: 0.202
- Space Group: I 4
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 193.398 | α = 90 |
| b = 193.398 | β = 90 |
| c = 58.208 | γ = 90 |
| Software Name | Purpose |
|---|---|
| SCALA | data scaling |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| PHASER | phasing |
| XDS | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2016-12-07 Deposition Author(s): Balaev, V.V., Lashkov, A.A., Gabdulkhakov, A.G., Betzel, C., Mikhailov, A.M.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Russian Foundation for Basic Research | Russian Federation | 14-04-00952 |
Revision History (Full details and data files)
- Version 1.0: 2016-12-07
Type: Initial release - Version 1.1: 2017-09-13
Changes: Advisory, Author supporting evidence - Version 1.2: 2024-01-10
Changes: Advisory, Data collection, Database references, Refinement description
