Download MendeleyCrystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2
Chang, C., Michalska, K., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Kim, Y., Joachimiak, A.To be published.
6VYO
Crystal structure of RNA binding domain of nucleocapsid phosphoprotein from SARS coronavirus 2
- PDB DOI: 10.2210/pdb6VYO/pdb
- Classification: VIRAL PROTEIN
- Organism(s): Severe acute respiratory syndrome coronavirus 2
- Expression System: Escherichia coli BL21(DE3)
- Mutation(s): No
- Deposited: 2020-02-27 Released: 2020-03-11
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.205
- R-Value Work: 0.159
- R-Value Observed: 0.162
wwPDB Validation 3D Report Full Report
This is version 3.0 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 |
| Nucleoprotein | A, B, C, D | 128 | Severe acute respiratory syndrome coronavirus 2 | Mutation(s): 0 Gene Names: N |  |
UniProt | |||||
Find proteins for P0DTC9 (Severe acute respiratory syndrome coronavirus 2) Explore P0DTC9 Go to UniProtKB: P0DTC9 | |||||
Entity Groups | |||||
| Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
| UniProt Group | P0DTC9 | ||||
Protein Feature ViewExpand | |||||
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Small Molecules
| Ligands 4 Unique | |||||
|---|---|---|---|---|---|
| ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
| MES Query on MES | E [auth A], G [auth A], L [auth B], Q [auth C] | 2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N |  | Ligand Interaction | |
| GOL Query on GOL | K [auth B], P [auth C], S [auth D], T [auth D] | GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N |  | Ligand Interaction | |
| ZN Query on ZN | H [auth A], J [auth A], M [auth B], R [auth C] | ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N |  | Ligand Interaction | |
| CL Query on CL | F [auth A], I [auth A], N [auth C], O [auth C] | CHLORIDE ION Cl VEXZGXHMUGYJMC-UHFFFAOYSA-M |  | Ligand Interaction | |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 1.70 Å
- R-Value Free: 0.205
- R-Value Work: 0.159
- R-Value Observed: 0.162
- Space Group: P 21 21 21
- Diffraction Data DOI: 10.18430/m36vyo Protein Diffraction
Unit Cell:
| Length ( Å ) | Angle ( ˚ ) |
|---|---|
| a = 66.238 | α = 90 |
| b = 77.43 | β = 90 |
| c = 114.039 | γ = 90 |
| Software Name | Purpose |
|---|---|
| PHENIX | refinement |
| SCALEPACK | data scaling |
| PDB_EXTRACT | data extraction |
| HKL-3000 | data reduction |
| HKL-3000 | phasing |
| SBC-Collect | data collection |
Entry History
Deposition Data
- Released Date: 2020-03-11 Deposition Author(s): Chang, C., Michalska, K., Jedrzejczak, R., Maltseva, N., Endres, M., Godzik, A., Kim, Y., Joachimiak, A., Center for Structural Genomics of Infectious Diseases (CSGID)
Revision History (Full details and data files)
- Version 1.0: 2020-03-11
Type: Initial release - Version 1.1: 2020-03-25
Changes: Structure summary - Version 2.0: 2020-04-08
Type: Coordinate replacement
Reason: Ligand identity
Changes: Advisory, Atomic model, Data collection, Derived calculations, Non-polymer description, Refinement description, Structure summary - Version 3.0: 2020-05-06
Changes: Atomic model, Data collection, Database references, Derived calculations, Source and taxonomy, Structure summary
