Research workbench
C-terminal domain of MERS-CoV nucleocapsid
Analyse C-terminal domain of MERS-CoV nucleocapsid in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6G13
- Type
- protein
- Length
- 452 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.97
- Source
- Middle East respiratory syndrome-related coronavirus
- Molecule
- Nucleoprotein
- UniProt
- A0A0D3MU51
- Ligands
- TMO, CL
- Pockets
- 5 · best druggability 0.77
Structure
x-ray diffraction · resolution 1.97 · 3 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 112 | 41% helix, 19% strand | A0A0D3MU51 |
| B, C | Nucleoprotein | protein | 113 | 41% helix, 19% strand | A0A0D3MU51 |
| D | Nucleoprotein | protein | 114 | 40% helix, 25% strand | A0A0D3MU51 |
Ligands and binding sites
- TMO · trimethylamine oxide · ligand · 4 copies · chains A, B, C
- CL · Chloride ion · ion · chains B
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 704 | 0.77 | 0.81 | 61 | empty |
| 2 | 65 | 0.38 | 0.79 | 17 | empty |
| 3 | 67 | 0.37 | 0.78 | 17 | empty |
| 4 | 95 | 0.36 | 0.74 | 18 | TMO |
| 5 | 66 | 0.33 | 0.76 | 18 | empty |
Interfaces
4 interfaces between chains.
- B–D · 2905 Ų buried · 45 hydrogen bonds · protein-protein
- A–C · 2805 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 520 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 313 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6G13 · C-terminal domain of MERS-cov nucleocapsid · 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 A0A0D3MU51
- Elsewhere: RCSB PDB 6G13 · PDBe 6G13 · UniProt A0A0D3MU51
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