Download MendeleyCrystal Structure of Prolyl-tRNA Synthetase from Onchocerca volvulus with bound Halofuginone and nucleotide
Dranow, D.M., Conrady, D.G., Lorimer, D.D., Horanyi, P.S., Edwards, T.E.To be published.
6MN8
Crystal Structure of Prolyl-tRNA Synthetase from Onchocerca volvulus with bound Halofuginone and nucleotide
- PDB DOI: https://doi.org/10.2210/pdb6MN8/pdb
- Classification: LIGASE
- Organism(s): Onchocerca volvulus
- Expression System: Escherichia coli
- Mutation(s): No
- Deposited: 2018-10-01 Released: 2018-10-17
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.35 Å
- R-Value Free: 0.179
- R-Value Work: 0.142
- R-Value Observed: 0.144
wwPDB Validation 3D Report Full Report
Currently 6MN8 does not have a validation slider image.
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 |
| Uncharacterized protein | 505 | Onchocerca volvulus | Mutation(s): 0 |  | |
UniProt | |||||
Find proteins for A0A2K6VKP7 (Onchocerca volvulus) Explore A0A2K6VKP7 Go to UniProtKB: A0A2K6VKP7 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | A0A2K6VKP7 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
| Ligands 7 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| ANP (Subject of Investigation/LOI) Query on ANP | E [auth A] | PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER C10 H17 N6 O12 P3 PVKSNHVPLWYQGJ-KQYNXXCUSA-N |  | ||
| HFG (Subject of Investigation/LOI) Query on HFG | D [auth A] | 7-bromo-6-chloro-3-{3-[(2R,3S)-3-hydroxypiperidin-2-yl]-2-oxopropyl}quinazolin-4(3H)-one C16 H17 Br Cl N3 O3 LVASCWIMLIKXLA-CABCVRRESA-N |  | ||
| AMP (Subject of Investigation/LOI) Query on AMP | F [auth A] | ADENOSINE MONOPHOSPHATE C10 H14 N5 O7 P UDMBCSSLTHHNCD-KQYNXXCUSA-N |  | ||
| 2PN (Subject of Investigation/LOI) Query on 2PN | G [auth A] | IMIDODIPHOSPHORIC ACID H5 N O6 P2 GNGSOPFGGKKDQP-UHFFFAOYSA-N |  | ||
| SER Query on SER | K [auth A], L [auth A] | SERINE C3 H7 N O3 MTCFGRXMJLQNBG-REOHCLBHSA-N |  | ||
| GLY Query on GLY | H [auth A], I [auth A], J [auth A] | GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N |  | ||
| MG Query on MG | B [auth A], C [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |  | ||
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.35 Å
- R-Value Free: 0.179
- R-Value Work: 0.142
- R-Value Observed: 0.144
- Space Group: H 3 2
- Diffraction Data: https://doi.org/10.18430/m36mn8
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 159.72 | α = 90 |
| b = 159.72 | β = 90 |
| c = 143.72 | γ = 120 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| XDS | data reduction |
| XSCALE | data scaling |
| PDB_EXTRACT | data extraction |
| MoRDa | phasing |
Structure Validation
Currently 6MN8 does not have a validation slider image.
Entry History
Deposition Data
- Released Date: 2018-10-17 Deposition Author(s): Seattle Structural Genomics Center for Infectious Disease (SSGCID)
Revision History (Full details and data files)
- Version 1.0: 2018-10-17
Type: Initial release - Version 1.1: 2023-10-11
Changes: Data collection, Database references, Derived calculations, Refinement description
