MolNFT v1 · #190526 · protein
Tail structure of bacteriophage SSV19
7XDI · VP1: “Tail structure of bacteriophage SSV19”. Electron microscopy, 10 pockets (best druggability 0.79). MolNFT v1 #190526 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7XDI
- Type
- protein
- Length
- 972 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- VP1; C131; B210; VP4
- UniProt
- A0A5Q0V137, A0A5Q0V0G9, A0A5Q0V0F6, A0A5Q0V0A2
- Pockets
- 10 · best druggability 0.79
Structure
electron microscopy · 4 distinct chains · 52% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | VP1 | protein | 69 | 84% helix, 0% strand | A0A5Q0V137 |
| D | C131 | protein | 124 | 66% helix, 6% strand | A0A5Q0V0G9 |
| E | B210 | protein | 185 | 31% helix, 29% strand | A0A5Q0V0F6 |
| F | VP4 | protein | 456 | 52% helix, 13% strand | A0A5Q0V0A2 |
Pockets
10 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 976 | 0.79 | 0.80 | 50 | empty |
| 2 | 373 | 0.57 | 0.74 | 34 | empty |
| 3 | 106 | 0.46 | 0.79 | 17 | empty |
| 4 | 194 | 0.44 | 0.73 | 25 | empty |
| 5 | 166 | 0.43 | 0.74 | 24 | empty |
Interfaces
6 interfaces between chains.
- D–E · 1540 Ų buried · 5 hydrogen bonds · protein-protein
- E–F · 1280 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 1148 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 1088 Ų buried · 2 hydrogen bonds · protein-protein
- A–F · 556 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7XDI · Tail structure of bacteriophage SSV19 · 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 A0A5Q0V137
- Every structure of UniProt A0A5Q0V0G9
- Every structure of UniProt A0A5Q0V0F6
- Every structure of UniProt A0A5Q0V0A2
- Elsewhere: RCSB PDB 7XDI · PDBe 7XDI · UniProt A0A5Q0V137 · UniProt A0A5Q0V0G9 · UniProt A0A5Q0V0F6 · UniProt A0A5Q0V0A2
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