MolNFT v1 · #188052 · protein
Crystal structure of the NSP3 bsm (betacoronavirus-specific marker) domain from SARS-cov-2
7T9W · Papain-like protease NSP3: “Crystal structure of the NSP3 bsm (betacoronavirus-specific marker) domain from SARS-cov-2”. X-ray diffraction, 1 ligand (CL), 14 pockets (best druggability 0.54). MolNFT v1 #188052 on GenesisL1: 3D…
- PDB
- 7T9W
- Type
- protein
- Length
- 1,430 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain-like protease NSP3
- EC
- 3.4.19.12, 3.4.22.-
- UniProt
- P0DTD1
- Ligands
- CL
- Pockets
- 14 · best druggability 0.54
Structure
x-ray diffraction · 7 distinct chains · 37% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F, I, L | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 88 | 33% helix, 18% strand | P0DTD1 |
| B | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 92 | 37% helix, 18% strand | P0DTD1 |
| C, G, N, O | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 90 | 38% helix, 21% strand | P0DTD1 |
| D, E, J, K | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 89 | 38% helix, 18% strand | P0DTD1 |
| H | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 91 | 37% helix, 19% strand | P0DTD1 |
| M | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 90 | 38% helix, 19% strand | P0DTD1 |
| P | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 89 | 38% helix, 19% strand | P0DTD1 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 332 | 0.54 | 0.74 | 47 | empty |
| 2 | 226 | 0.49 | 0.75 | 35 | empty |
| 3 | 201 | 0.49 | 0.76 | 30 | empty |
| 4 | 205 | 0.48 | 0.75 | 40 | empty |
| 5 | 188 | 0.46 | 0.75 | 33 | empty |
Interfaces
26 interfaces between chains.
- A–N · 427 Ų buried · 1 hydrogen bond · protein-protein
- D–O · 423 Ų buried · 2 hydrogen bonds · protein-protein
- H–P · 420 Ų buried · 2 hydrogen bonds · protein-protein
- B–M · 419 Ų buried · 2 hydrogen bonds · protein-protein
- E–J · 419 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 7T9W · Crystal structure of the Nsp3 bSM (Betacoronavirus-Specific Marker) domain from SARS-CoV-2 · 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 P0DTD1
- Elsewhere: RCSB PDB 7T9W · PDBe 7T9W · UniProt P0DTD1
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