MolNFT v1 · #169578 · protein
YSD1_17 major capsid protein
6XGP: “YSD1_17 major capsid protein”. X-ray diffraction, 6 pockets (best druggability 0.61). MolNFT v1 #169578 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XGP
- Type
- protein
- Length
- 657 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YSD1_17 major capsid protein
- UniProt
- A0A498U580
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | YSD1_17 major capsid protein | protein | 327 | 28% helix, 29% strand | A0A498U580 |
| B | YSD1_17 major capsid protein | protein | 330 | 28% helix, 30% strand | A0A498U580 |
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 | 449 | 0.61 | 0.75 | 56 | empty |
| 2 | 369 | 0.56 | 0.75 | 50 | empty |
| 3 | 287 | 0.53 | 0.75 | 31 | empty |
| 4 | 97 | 0.45 | 0.79 | 17 | empty |
| 5 | 92 | 0.43 | 0.78 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 315 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6XGP · YSD1_17 major capsid 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 A0A498U580
- Elsewhere: RCSB PDB 6XGP · PDBe 6XGP · UniProt A0A498U580
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