Download MendeleyThe structure of the C146A variant of the amidase from Pyrococcus horikoshii bound to glutaramide suggests the basis of amide recognition.
Sewell, B.T., Su, S., Venter, P., Makumire, S.To be published.
6YPA
The C146A variant of an amidase from Pyrococcus horikoshii with bound glutaramide
- PDB DOI: https://doi.org/10.2210/pdb6YPA/pdb
- Classification: HYDROLASE
- Organism(s): Pyrococcus horikoshii
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): Yes
- Deposited: 2020-04-15 Released: 2020-06-03
- Funding Organization(s): Global Challenges Research Fund
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.58 ?
- R-Value Free: 0.240
- R-Value Work: 0.206
- R-Value Observed: 0.208
Starting Model: experimental
View more details
This is version 1.1 of the entry. See complete history.
Re-refinement Note
A newer entry is available that reflects an alternative modeling of the original data: 7OVG
Literature
To be published.
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
|---|---|---|---|---|---|
| Molecule | Chains | Sequence Length | Organism | Details | Image |
| CN hydrolase domain-containing protein | 282 | Pyrococcus horikoshii | Mutation(s): 1 Gene Names: PH0642 |  | |
UniProt | |||||
Find proteins for O58376 (Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)) Explore O58376 Go to UniProtKB: O58376 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | O58376 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| P6W (Subject of Investigation/LOI) Query on P6W | E [auth A], G [auth B], H [auth C], I [auth D] | pentanediamide C5 H10 N2 O2 RCCYSVYHULFYHE-UHFFFAOYSA-N |  | ||
| GOL Query on GOL | F [auth A] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.58 ?
- R-Value Free: 0.240
- R-Value Work: 0.206
- R-Value Observed: 0.208
- Space Group: P 21 21 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 77.684 | ¦Á = 90 |
| b = 100.639 | ¦Â = 90 |
| c = 134.096 | ¦Ă = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| xia2 | data scaling |
| PHASER | phasing |
| PDB_EXTRACT | data extraction |
| DIALS | data reduction |
Entry History & Funding Information
Deposition Data
- Released Date: 2020-06-03 Deposition Author(s): Sewell, B.T., Su, S., Venter, P., Makumire, S.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Global Challenges Research Fund | United Kingdom | ST/R002754/1 |
Revision History (Full details and data files)
- Version 1.0: 2020-06-03
Type: Initial release - Version 1.1: 2024-01-24
Changes: Data collection, Database references, Refinement description
