MolNFT v2 · #225692 · protein
SARS-CoV-2 DMV nsp3-4 pore complex (consensus-pore, C6 symmetry)
8YB5 · Papain-like protease nsp3: “SARS-CoV-2 DMV nsp3-4 pore complex (consensus-pore, C6 symmetry)”. Electron microscopy at 4.2, 20 pockets (best druggability 0.63). MolNFT v2 #225692 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 8YB5
- Type
- protein
- Length
- 1,456 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 4.2
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Papain-like protease nsp3; Non-structural protein 4
- EC
- 3.4.19.12
- UniProt
- P0DTD1
- Pockets
- 20 · best druggability 0.63
Structure
electron microscopy · resolution 4.2 · 3 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain-like protease nsp3 (EC 3.4.19.12) | protein | 353 | 45% helix, 15% strand | P0DTD1 |
| B | Papain-like protease nsp3 (EC 3.4.19.12) | protein | 361 | 44% helix, 15% strand | P0DTD1 |
| C, D | Non-structural protein 4 | protein | 371 | 37% helix, 22% strand | P0DTD1 |
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 253 | 0.63 | 0.81 | 33 | empty |
| 2 | 238 | 0.63 | 0.82 | 35 | empty |
| 3 | 303 | 0.63 | 0.79 | 39 | empty |
| 4 | 268 | 0.61 | 0.80 | 29 | empty |
| 5 | 152 | 0.57 | 0.82 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–C · 1260 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 1123 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 543 Ų buried · 3 hydrogen bonds · protein-protein
- C–D · 454 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 120 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 13 disulfide (disulfide).
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 P0DTD1
- Elsewhere: RCSB PDB 8YB5 · PDBe 8YB5 · UniProt P0DTD1
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