Research workbench
P3, the major coat protein of the lipid-containing bacteriophage PRD1.
Analyse P3, the major coat protein of the lipid-containing bacteriophage PRD1. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HX6
- Type
- protein
- Length
- 1,115 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Major capsid protein
- UniProt
- P22535
- Ligands
- NA, CL
- Pockets
- 10 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Major capsid protein | protein | 370 | 14% helix, 43% strand | P22535 |
| B | Major capsid protein | protein | 374 | 14% helix, 43% strand | P22535 |
| C | Major capsid protein | protein | 371 | 16% helix, 43% strand | P22535 |
Ligands and binding sites
- NA · Sodium ion · metal · 7 copies · chains A, B, C
- CL · Chloride ion · ion · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 18 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 486 | 0.78 | 0.86 | 41 | MPD |
| 2 | 467 | 0.76 | 0.84 | 44 | MPD |
| 3 | 458 | 0.76 | 0.85 | 50 | MPD |
| 4 | 85 | 0.54 | 0.85 | 20 | empty |
| 5 | 251 | 0.49 | 0.74 | 34 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1872 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 1784 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 1780 Ų buried · 33 hydrogen bonds · protein-protein
Compared structures
- 1HX6 · P3, the major coat protein of the lipid-containing bacteriophage PRD1. · 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 P22535
- Elsewhere: RCSB PDB 1HX6 · PDBe 1HX6 · UniProt P22535
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