MolNFT v1 · #169579 · protein
YSD1 bacteriophage capsid
6XGQ · YSD1_17: “YSD1 bacteriophage capsid”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #169579 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6XGQ
- Type
- protein
- Length
- 3,318 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- YSD1_17; YSD1_16
- UniProt
- A0A498U580, A0A498TZZ8
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 19% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | YSD1_17 | protein | 353 | 20% helix, 30% strand | A0A498U580 |
| G | YSD1_17 | protein | 332 | 22% helix, 24% strand | A0A498U580 |
| a, b, c, d, e, f, g | YSD1_16 | protein | 124 | 8% helix, 27% strand | A0A498TZZ8 |
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1177 | 0.81 | 0.82 | 99 | empty |
| 2 | 335 | 0.73 | 0.85 | 31 | empty |
| 3 | 687 | 0.72 | 0.79 | 80 | empty |
| 4 | 456 | 0.66 | 0.79 | 48 | empty |
| 5 | 489 | 0.65 | 0.78 | 59 | empty |
Interfaces
35 interfaces between chains.
- D–E · 3634 Ų buried · 47 hydrogen bonds · protein-protein
- C–D · 3558 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 3512 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 3484 Ų buried · 42 hydrogen bonds · protein-protein
- E–F · 3429 Ų buried · 46 hydrogen bonds · protein-protein
Compared structures
- 6XGQ · YSD1 bacteriophage capsid · 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
- Every structure of UniProt A0A498TZZ8
- Elsewhere: RCSB PDB 6XGQ · PDBe 6XGQ · UniProt A0A498U580 · UniProt A0A498TZZ8
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