MolNFT v1 · #188217 · protein
Sud-C and UBL2 domains of SARS cov-2 NSP3 protein
7THH · Papain-like protease NSP3: “Sud-C and UBL2 domains of SARS cov-2 NSP3 protein”. X-ray diffraction, 2 ligands (CL, IOD), 6 pockets (best druggability 0.64). MolNFT v1 #188217 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7THH
- Type
- protein
- Length
- 783 residues
- Chains
- 6
- 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, IOD
- Pockets
- 6 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 22% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 131 | 22% helix, 37% strand | P0DTD1 |
| B, E | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 130 | 22% helix, 38% strand | P0DTD1 |
| F | Papain-like protease NSP3 (EC 3.4.19.12, 3.4.22.-) | protein | 130 | 22% helix, 40% strand | P0DTD1 |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains A, E, F
- IOD · Iodide ion · ion · 3 copies · chains B, C
- P6G · Hexaethylene glycol · additive · 3 copies · chains A, E, B, C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 641 | 0.64 | 0.75 | 59 | empty |
| 2 | 448 | 0.59 | 0.75 | 40 | empty |
| 3 | 320 | 0.57 | 0.76 | 40 | P6G |
| 4 | 184 | 0.46 | 0.76 | 31 | CL |
| 5 | 189 | 0.46 | 0.75 | 22 | empty |
Interfaces
7 interfaces between chains.
- D–E · 620 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 562 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 522 Ų buried · 3 hydrogen bonds · protein-protein
- E–F · 453 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 244 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 7THH · SUD-C and Ubl2 domains of SARS CoV-2 Nsp3 protein · 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 7THH · PDBe 7THH · UniProt P0DTD1
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