Research workbench
Atomic models of P1, P4 C-terminal fragment and P8 fitted in the bacteriophage PHI6 nucleocapsid reconstructed with icosahedral symmetry
Analyse Atomic models of P1, P4 C-terminal fragment and P8 fitted in the bacteriophage… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6HY0
- Type
- protein
- Length
- 3,051 residues
- Chains
- 13
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major inner protein P1; Packaging enzyme P4; Major outer capsid protein P8
- UniProt
- P11126, P11125, P07579
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Major inner protein P1 | protein | 766 | 47% helix, 13% strand | P11126 |
| C | Packaging enzyme P4 | protein | 39 | 10% helix, 5% strand | P11125 |
| D, E, F, G, H, I, J, K, L, M | Major outer capsid protein P8 | protein | 148 | 75% helix, 0% strand | P07579 |
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 | 902 | 0.85 | 0.87 | 104 | empty |
| 2 | 922 | 0.83 | 0.84 | 97 | empty |
| 3 | 312 | 0.80 | 0.90 | 46 | empty |
| 4 | 573 | 0.78 | 0.84 | 80 | empty |
| 5 | 446 | 0.74 | 0.84 | 67 | empty |
Interfaces
33 interfaces between chains.
- B–C · 1711 Ų buried · 17 hydrogen bonds · protein-protein
- K–M · 1472 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1353 Ų buried · 10 hydrogen bonds · protein-protein
- F–G · 1031 Ų buried · 10 hydrogen bonds · protein-protein
- L–M · 1020 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 6HY0 · Atomic models of P1, P4 C-terminal fragment and P8 fitted in the bacteriophage phi6… · 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 P11126
- Every structure of UniProt P11125
- Every structure of UniProt P07579
- Elsewhere: RCSB PDB 6HY0 · PDBe 6HY0 · UniProt P11126 · UniProt P11125 · UniProt P07579
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