Download MendeleyPanDDA analysis group deposition
Tham, C.T., Coker, J.A., Krojer, T., Foster, W.R., Koekemoer, L., Douangamath, A., Talon, R., Fearon, D., von Delft, F., Yue, W.W., Bountra, C., Bezerra, G.A.To be published.
5SDO | pdb_00005sdo
PanDDA analysis group deposition -- Crystal Structure of Porphyromonas gingivalis in complex with Z19735067
- PDB DOI: https://doi.org/10.2210/pdb5SDO/pdb
- Deposition Group: G_1002227 (changed state) ExploreG_1002227
- Classification: HYDROLASE
- Organism(s): Porphyromonas gingivalis
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2022-01-20 Released: 2022-02-09
- Funding Organization(s): University of Oxford
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 ?
- R-Value Free: 0.241 (Depositor), 0.250 (DCC)
- R-Value Work: 0.221 (Depositor), 0.220 (DCC)
- R-Value Observed: 0.222 (Depositor)
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 |
| Asp/Glu-specific dipeptidyl-peptidase | 707 | Porphyromonas gingivalis | Mutation(s): 0 Gene Names: dpp11, PGN_0607 EC: 3.4.14 |  | |
UniProt | |||||
Find proteins for B2RID1 (Porphyromonas gingivalis (strain ATCC 33277 / DSM 20709 / CIP 103683 / JCM 12257 / NCTC 11834 / 2561)) Explore B2RID1 Go to UniProtKB: B2RID1 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | B2RID1 | ||||
Sequence AnnotationsExpand | |||||
| |||||
Small Molecules
| Ligands 2 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| I8G (Subject of Investigation/LOI) Query on I8G | C [auth A], F [auth A], G [auth B] | 2-(4-fluorophenoxy)-1-(pyrrolidin-1-yl)ethan-1-one C12 H14 F N O2 AJVMKMWCEVOBPX-UHFFFAOYSA-N |  | ||
| CL Query on CL | D [auth A], E [auth A], H [auth B] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.05 ?
- R-Value Free: 0.241 (Depositor), 0.250 (DCC)
- R-Value Work: 0.221 (Depositor), 0.220 (DCC)
- R-Value Observed: 0.222 (Depositor)
Space Group: P 21 21 21
Unit Cell:
| Length ( ? ) | Angle ( ? ) |
|---|---|
| a = 101.802 | α = 90 |
| b = 117.06 | β = 90 |
| c = 147.933 | γ = 90 |
| Software Name | Purpose |
|---|---|
| BUSTER | refinement |
| Aimless | data scaling |
| PDB_EXTRACT | data extraction |
| XDS | data reduction |
| PHASER | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2022-02-09 Deposition Author(s): Tham, C.T., Coker, J.A., Krojer, T., Foster, W.R., Koekemoer, L., Douangamath, A., Talon, R., Fearon, D., von Delft, F., Yue, W.W., Bountra, C., Bezerra, G.A.
| Funding Organization | Location | Grant Number |
|---|---|---|
| University of Oxford | United Kingdom | 0006369 |
Revision History (Full details and data files)
- Version 1.0: 2022-02-09
Type: Initial release - Version 1.1: 2024-10-23
Changes: Data collection, Structure summary
