Download MendeleyStructure of Protein serine/threonine phosphatase from Saccharomyces cerevisiae with similarity to human phosphatase PP5
Singer, A.U., Xu, X., Chang, C., Cui, H., Edwards, A.M., Joachimiak, A., Savchenko, A., Yakunin, A.F.To be published.
3ICF
Structure of Protein serine/threonine phosphatase from Saccharomyces cerevisiae with similarity to human phosphatase PP5
- PDB DOI: https://doi.org/10.2210/pdb3ICF/pdb
- Classification: HYDROLASE
- Organism(s): Saccharomyces cerevisiae
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2009-07-17 Released: 2009-08-25
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.240
- R-Value Work: 0.190
- R-Value Observed: 0.192
wwPDB Validation 3D Report Full Report
This is version 1.3 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 |
| Serine/threonine-protein phosphatase T | 335 | Saccharomyces cerevisiae | Mutation(s): 0 Gene Names: G6347, PPT1, YGR123C EC: 3.1.3.16 |  | |
UniProt | |||||
Find proteins for P53043 (Saccharomyces cerevisiae (strain ATCC 204508 / S288c)) Explore P53043 Go to UniProtKB: P53043 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P53043 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 5 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PO4 Query on PO4 | E [auth A], J [auth B] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| EDO Query on EDO | F [auth A], K [auth B] | 1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N |  | ||
| FE Query on FE | C [auth A], D [auth A], H [auth B], I [auth B] | FE (III) ION Fe VTLYFUHAOXGGBS-UHFFFAOYSA-N |  | ||
| CL Query on CL | L [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
| NA Query on NA | G [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A, B | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.30 Å
- R-Value Free: 0.240
- R-Value Work: 0.190
- R-Value Observed: 0.192
- Space Group: P 32
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 47.194 | α = 90 |
| b = 47.194 | β = 90 |
| c = 237.096 | γ = 120 |
| Software Name | Purpose |
|---|---|
| SBC-Collect | data collection |
| PHASER | phasing |
| REFMAC | refinement |
| HKL-3000 | data reduction |
| HKL-2000 | data scaling |
Entry History
Deposition Data
- Released Date: 2009-08-25 Deposition Author(s): Singer, A.U., Xu, X., Chang, C., Cui, H., Kagan, O., Edwards, A.M., Joachimiak, A., Yakunin, A.F., Savchenko, A., Midwest Center for Structural Genomics (MCSG)
Revision History (Full details and data files)
- Version 1.0: 2009-08-25
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2023-09-06
Changes: Data collection, Database references, Derived calculations, Refinement description - Version 1.3: 2023-11-22
Changes: Data collection
