Research workbench
Structural studies of bacteriophage ALPHA3 assembly, X-ray crystallography
Analyse Structural studies of bacteriophage ALPHA3 assembly, X-ray crystallography in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1M06
- Type
- protein + DNA
- Length
- 639 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Capsid protein; Major spike protein; Small core protein…
- UniProt
- P08767, P31281, P08766
- Ligands
- 3DR
- Pockets
- 7 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Capsid protein | protein | 422 | 26% helix, 29% strand | P08767 |
| G | Major spike protein | protein | 187 | 2% helix, 49% strand | P31281 |
| J | Small core protein | protein | 24 | 13% helix, 0% strand | P08766 |
| X | 5'-D(P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR)P*(3DR) P*(3DR)P*(3DR)P*(3DR))-3' | dna | 6 | — | — |
Ligands and binding sites
- 3DR · 1',2'-dideoxyribofuranose-5'-phosphate · ligand · 4 copies · chains F, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 282 | 0.73 | 0.86 | 40 | empty |
| 2 | 197 | 0.49 | 0.75 | 26 | empty |
| 3 | 62 | 0.39 | 0.80 | 25 | empty |
| 4 | 129 | 0.37 | 0.73 | 27 | empty |
| 5 | 58 | 0.33 | 0.77 | 13 | empty |
Interfaces
4 interfaces between chains.
- F–J · 1246 Ų buried · 13 hydrogen bonds · protein-protein
- J–X · 450 Ų buried · 9 hydrogen bonds · protein-nucleic
- F–X · 318 Ų buried · 9 hydrogen bonds · protein-nucleic
- F–G · 209 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified, 1 covalent (nucleotide modification, covalent ligand).
Compared structures
- 1M06 · Structural Studies of Bacteriophage alpha3 Assembly, X-Ray Crystallography · the same entry in another collection · chain G against G, 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 P08767
- Every structure of UniProt P31281
- Every structure of UniProt P08766
- Elsewhere: RCSB PDB 1M06 · PDBe 1M06 · UniProt P08767 · UniProt P31281 · UniProt P08766
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.