Download MendeleyCrystal structure of proline dipeptidase from Pyrococcus furiosus complexed with Mn
Kinkar, O.U., Chandravanshi, K., Kumar, A., Makde, R.D.To be published.
9KWA | pdb_00009kwa
Crystal structure of proline dipeptidase from Pyrococcus furiosus complexed with Mn
- PDB DOI: https://doi.org/10.2210/pdb9KWA/pdb
- Classification: HYDROLASE
- Organism(s): Pyrococcus furiosus DSM 3638
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2024-12-05 Released: 2025-12-10
- Funding Organization(s): Department of Science & Technology (DST, India)
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.211 (Depositor), 0.213 (DCC)
- R-Value Work: 0.178 (Depositor), 0.177 (DCC)
- R-Value Observed: 0.180 (Depositor)
Starting Model: in silico
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This is version 1.0 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 | 394 | Pyrococcus furiosus DSM 3638 | Mutation(s): 0 Gene Names: PF0747 |  | |
UniProt | |||||
Find proteins for Q8U2T3 (Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422 / Vc1)) Explore Q8U2T3 Go to UniProtKB: Q8U2T3 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | Q8U2T3 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 3 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| PEG (Subject of Investigation/LOI) Query on PEG | E [auth A], H [auth B] | DI(HYDROXYETHYL)ETHER C4 H10 O3 MTHSVFCYNBDYFN-UHFFFAOYSA-N |  | ||
| MN (Subject of Investigation/LOI) Query on MN | C [auth A], F [auth B] | MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N |  | ||
| NA (Subject of Investigation/LOI) Query on NA | D [auth A], G [auth B] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.85 Å
- R-Value Free: 0.211 (Depositor), 0.213 (DCC)
- R-Value Work: 0.178 (Depositor), 0.177 (DCC)
- R-Value Observed: 0.180 (Depositor)
Space Group: P 1 21 1
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 61.272 | α = 90 |
| b = 71.589 | β = 92.836 |
| c = 89.196 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| Aimless | data scaling |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2025-12-10 Deposition Author(s): Kinkar, O.U., Chandravanshi, K., Kumar, A., Makde, R.D.
| Funding Organization | Location | Grant Number |
|---|---|---|
| Department of Science & Technology (DST, India) | India | -- |
Revision History (Full details and data files)
- Version 1.0: 2025-12-10
Type: Initial release
