Download MendeleyCrystal structure of pyrimidine 5 -nucleotidase SDT1 from Saccharomyces cerevisiae complexed with uridine 5'-monophosphate
Shi, N., Teng, M.K., Niu, L.W.To be published.
3OPX | pdb_00003opx
Crystal structure of pyrimidine 5 -nucleotidase SDT1 from Saccharomyces cerevisiae complexed with uridine 5'-monophosphate
- PDB DOI: https://doi.org/10.2210/pdb3OPX/pdb
- Classification: HYDROLASE
- Organism(s): Saccharomyces cerevisiae
- Expression System: Escherichia coli
- Mutation(s): Yes
- Deposited: 2010-09-02 Released: 2011-03-02
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.251 (Depositor), 0.250 (DCC)
- R-Value Work: 0.212 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.214 (Depositor)
Starting Model: experimental
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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 |
| Protein SSM1 | 263 | Saccharomyces cerevisiae | Mutation(s): 1 Gene Names: SSM1, SDT1, YGL224C |  | |
UniProt | |||||
Find proteins for P53078 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53078 Go to UniProtKB: P53078 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P53078 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| U5P Query on U5P | C [auth A] | URIDINE-5'-MONOPHOSPHATE C9 H13 N2 O9 P DJJCXFVJDGTHFX-XVFCMESISA-N |  | ||
| MG Query on MG | B [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.251 (Depositor), 0.250 (DCC)
- R-Value Work: 0.212 (Depositor), 0.210 (DCC)
- R-Value Observed: 0.214 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 41.198 | α = 90 |
| b = 78.037 | β = 90 |
| c = 82.789 | γ = 90 |
| Software Name | Purpose |
|---|---|
| MAR345dtb | data collection |
| MOLREP | phasing |
| PHENIX | refinement |
| HKL-2000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2011-03-02 Deposition Author(s): Teng, M.K., Niu, L.W., Shi, N.
Revision History (Full details and data files)
- Version 1.0: 2011-03-02
Type: Initial release - Version 1.1: 2011-07-13
Changes: Version format compliance - Version 1.2: 2023-11-01
Changes: Data collection, Database references, Derived calculations, Refinement description
