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 | pdb_00003icf
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 (Depositor), 0.240 (DCC)
- R-Value Work: 0.190 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.192 (Depositor)
Starting Model: experimental
View more details
wwPDB Validation 3D Report Full Report
This is version 1.4 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 (Depositor), 0.240 (DCC)
- R-Value Work: 0.190 (Depositor), 0.190 (DCC)
- R-Value Observed: 0.192 (Depositor)
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 - Version 1.4: 2024-10-30
Changes: Structure summary
