Download MendeleyProline dipeptidase from Deinococcus radiodurans R1 at 1.45 Angstrom resolution
Kumar, A., Are, V., Ghosh, B., Jamdar, S., Makde, R.To be published.
5CDV
Proline dipeptidase from Deinococcus radiodurans R1
- PDB DOI: https://doi.org/10.2210/pdb5CDV/pdb
- Classification: HYDROLASE
- Organism(s): Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2015-07-05 Released: 2016-08-10
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.198
- R-Value Work: 0.182
- R-Value Observed: 0.182
wwPDB Validation 3D Report Full Report
This is version 1.2 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 |
| Proline dipeptidase | 349 | Deinococcus radiodurans R1 = ATCC 13939 = DSM 20539 | Mutation(s): 0 Gene Names: DR_1246 |  | |
UniProt | |||||
Find proteins for Q9RUY4 (Deinococcus radiodurans (strain ATCC 13939 / DSM 20539 / JCM 16871 / CCUG 27074 / LMG 4051 / NBRC 15346 / NCIMB 9279 / VKM B-1422 / R1)) Explore Q9RUY4 Go to UniProtKB: Q9RUY4 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q9RUY4 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PO4 Query on PO4 | D [auth A], E [auth A], F [auth A], G [auth A], H [auth A] | PHOSPHATE ION O4 P NBIIXXVUZAFLBC-UHFFFAOYSA-K |  | ||
| MN Query on MN | B [auth A] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| NA Query on NA | C [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.45 Å
- R-Value Free: 0.198
- R-Value Work: 0.182
- R-Value Observed: 0.182
- Space Group: P 43 21 2
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 60.619 | α = 90 |
| b = 60.619 | β = 90 |
| c = 202.784 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| Coot | model building |
| PHENIX | model building |
| PHASER | phasing |
| Aimless | data scaling |
| XDS | data processing |
| MAR345dtb | data collection |
Entry History
Deposition Data
- Released Date: 2016-08-10 Deposition Author(s): Kumar, A., Are, V., Ghosh, B., Jamdar, S., Makde, R.
Revision History (Full details and data files)
- Version 1.0: 2016-08-10
Type: Initial release - Version 1.1: 2018-07-04
Changes: Data collection, Derived calculations - Version 1.2: 2023-11-08
Changes: Data collection, Database references, Derived calculations, Refinement description
