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Download EndnoteGlycosidase F290Y
Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.To be published.
5Z3D
Glycosidase F290Y
- DOI: 10.2210/pdb5Z3D/pdb
- Classification: HYDROLASE
- Organism(s): Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)
- Expression System: Escherichia coli
- Mutation(s): 1
- Deposited: 2018-01-05 Released: 2019-05-15
- Funding Organization(s): Platform for Drug Discovery, Informatics, and Structural Life Science(PDIS)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.25 Å
- R-Value Free: 0.134
- R-Value Work: 0.113
wwPDB Validation 3D Report Full Report
This is version 1.0 of the entry. See complete history.
Literature
Macromolecules
Find similar proteins by: Sequence | Structure
Entity ID: 1 | ||||
|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details |
| Glycoside hydrolase 15-related protein | A | 405 | Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399) | Mutation(s): 1 EC: 3.2.1.205 |
Find proteins for D2PPM8 (Kribbella flavida (strain DSM 17836 / JCM 10339 / NBRC 14399)) Go to UniProtKB: D2PPM8 | ||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| CIT Query on CIT | A | CITRIC ACID C6 H8 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-N |  | Ligand Interaction | |
| GOL Query on GOL | A | GLYCEROL GLYCERIN; PROPANE-1,2,3-TRIOL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| Modified Residues 1 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Type | Formula | 2D Diagram | Parent |
| CSD Query on CSD | A | L-PEPTIDE LINKING | C3 H7 N O4 S |  | CYS |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.25 Å
- R-Value Free: 0.134
- R-Value Work: 0.113
- Space Group: P 4 21 2
Unit Cell:
| Length (Å) | Angle (°) |
|---|---|
| a = 104.725 | α = 90.00 |
| b = 104.725 | β = 90.00 |
| c = 89.319 | γ = 90.00 |
| Software Name | Purpose |
|---|---|
| XDS | data scaling |
| XDS | data reduction |
| PHASER | phasing |
| REFMAC | refinement |
Entry History & Funding Information
Deposition Data
- Deposited Date: 2018-01-05
- Released Date: 2019-05-15
- Deposition Author(s): Tanaka, Y., Chen, M., Tagami, T., Yao, M., Kimura, A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Platform for Drug Discovery, Informatics, and Structural Life Science(PDIS) | Japan | -- |
Revision History
- Version 1.0: 2019-05-15
Type: Initial release
