MolNFT v1 · #162110 · protein
The crystal structure of head fiber GP8.5 N base in bacteriophage PHI29
6QYY · Capsid fiber protein: “The crystal structure of head fiber GP8.5 N base in bacteriophage PHI29”. X-ray diffraction, 1 ligand (SO4), 10 pockets (best druggability 0.77). MolNFT v1 #162110 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6QYY
- Type
- protein
- Length
- 709 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid fiber protein
- UniProt
- B3VMP4
- Ligands
- SO4
- Pockets
- 10 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Capsid fiber protein | protein | 119 | 5% helix, 45% strand | B3VMP4 |
| B, C, D, E, F | Capsid fiber protein | protein | 118 | 5% helix, 44% strand | B3VMP4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 281 | 0.77 | 0.89 | 42 | empty |
| 2 | 554 | 0.77 | 0.83 | 59 | empty |
| 3 | 380 | 0.68 | 0.81 | 42 | empty |
| 4 | 199 | 0.64 | 0.84 | 33 | empty |
| 5 | 218 | 0.63 | 0.82 | 36 | SO4 |
Interfaces
9 interfaces between chains.
- A–E · 863 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 780 Ų buried · 11 hydrogen bonds · protein-protein
- C–E · 741 Ų buried · 1 hydrogen bond · protein-protein
- D–F · 716 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 449 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 6QYY · The crystal structure of head fiber gp8.5 N base in bacteriophage phi29 · 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 B3VMP4
- Elsewhere: RCSB PDB 6QYY · PDBe 6QYY · UniProt B3VMP4
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