MolNFT v2 · #193332 · protein
Crystal structure of the Nsp3 Y3 domain from SARS-CoV-2
7RQG · Non-structural protein 3: “Crystal structure of the Nsp3 Y3 domain from SARS-CoV-2”. X-ray diffraction at 2.17, 3 pockets (best druggability 0.68). MolNFT v2 #193332 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7RQG
- Type
- protein
- Length
- 382 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.17
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Non-structural protein 3
- EC
- 3.4.19.12, 3.4.22.-
- UniProt
- P0DTD1
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · resolution 2.17 · 3 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 3 (EC 3.4.19.12, 3.4.22.-) | protein | 102 | 33% helix, 20% strand | P0DTD1 |
| B, C | Non-structural protein 3 (EC 3.4.19.12, 3.4.22.-) | protein | 100 | 36% helix, 21% strand | P0DTD1 |
| D | Non-structural protein 3 (EC 3.4.19.12, 3.4.22.-) | protein | 80 | 36% helix, 26% strand | P0DTD1 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.68 | 0.78 | 93 | empty |
| 2 | 63 | 0.38 | 0.79 | 17 | empty |
| 3 | 73 | 0.36 | 0.77 | 19 | empty |
Interfaces
5 interfaces between chains.
- A–C · 693 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 642 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 308 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 247 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7RQG · Crystal structure of the NSP3 Y3 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 7RQG · PDBe 7RQG · UniProt P0DTD1
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