Download MendeleyStructure of phage-associated cell wall hydrolase PlyPy from Streptococcus pyogenes
Edgar, R.J., Korotkova, N., Korotkov, K.V.To be published.
5UDM
Phage-associated cell wall hydrolase PlyPy from Streptococcus pyogenes, space group P6522
- PDB DOI: https://doi.org/10.2210/pdb5UDM/pdb
- Classification: HYDROLASE
- Organism(s): Streptococcus pyogenes MGAS5005
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2016-12-27 Released: 2017-12-27
- Funding Organization(s): National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID), National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.64 Å
- R-Value Free: 0.237
- R-Value Work: 0.210
- R-Value Observed: 0.211
wwPDB Validation 3D Report Full Report
This is version 1.1 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 |
| Phage-associated cell wall hydrolase | A [auth B], B [auth A] | 261 | Streptococcus pyogenes MGAS5005 | Mutation(s): 0 Gene Names: M5005_Spy1001 |  |
UniProt | |||||
Find proteins for J7M5V6 (Streptococcus pyogenes M1 476) Explore J7M5V6 Go to UniProtKB: J7M5V6 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | J7M5V6 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| GOL Query on GOL | C [auth B], D [auth B], E [auth A], F [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| MSE Query on MSE | A [auth B], B [auth A] | L-PEPTIDE LINKING | C5 H11 N O2 Se |  | MET |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.64 Å
- R-Value Free: 0.237
- R-Value Work: 0.210
- R-Value Observed: 0.211
- Space Group: P 65 2 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 122.97 | α = 90 |
| b = 122.97 | β = 90 |
| c = 163.73 | γ = 120 |
| Software Name | Purpose |
|---|---|
| XSCALE | data scaling |
| PHASER | phasing |
| PHENIX | refinement |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2017-12-27 Deposition Author(s): Edgar, R.J., Korotkova, N., Korotkov, K.V.
| Funding Organization | Location | Grant Number |
|---|---|---|
| National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID) | United States | 1R21AI113253 |
| National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS) | United States | P30GM110787 |
Revision History (Full details and data files)
- Version 1.0: 2017-12-27
Type: Initial release - Version 1.1: 2019-12-11
Changes: Author supporting evidence
