Research workbench
Crystal Structure of SARS-CoV-2 N-CTD in complex with GTP (I)
Analyse Crystal Structure of SARS-CoV-2 N-CTD in complex with GTP (I) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7O35
- Type
- protein
- Length
- 454 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.8
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Nucleoprotein
- UniProt
- P0DTC9
- Ligands
- GTP
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · resolution 1.8 · 3 distinct chains · 41% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Nucleoprotein | protein | 111 | 40% helix, 20% strand | P0DTC9 |
| B | Nucleoprotein | protein | 123 | 41% helix, 18% strand | P0DTC9 |
| D | Nucleoprotein | protein | 109 | 40% helix, 20% strand | P0DTC9 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 632 | 0.65 | 0.75 | 76 | empty |
| 2 | 85 | 0.40 | 0.78 | 21 | empty |
| 3 | 102 | 0.39 | 0.76 | 24 | empty |
| 4 | 88 | 0.37 | 0.76 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2678 Ų buried · 43 hydrogen bonds · protein-protein
- C–D · 2661 Ų buried · 46 hydrogen bonds · protein-protein
- B–D · 707 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 96 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 16 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 7O35 · Crystal structure of SARS-cov-2 N-ctd in complex with GTP (I) · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P0DTC9
- Elsewhere: RCSB PDB 7O35 · PDBe 7O35 · UniProt P0DTC9
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