Research workbench
Crystal structure of the bacteriophage PHI29 tail knob protein GP9 truncation variant
Analyse Crystal structure of the bacteriophage PHI29 tail knob protein GP9 truncation… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5FEI
- Type
- protein
- Length
- 1,021 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Distal tube protein
- UniProt
- P04331
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Distal tube protein | protein | 509 | 17% helix, 38% strand | P04331 |
| B | Distal tube protein | protein | 512 | 16% helix, 36% strand | P04331 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 792 | 0.75 | 0.80 | 80 | empty |
| 2 | 306 | 0.62 | 0.79 | 51 | empty |
| 3 | 257 | 0.56 | 0.78 | 37 | empty |
| 4 | 93 | 0.48 | 0.81 | 23 | empty |
| 5 | 56 | 0.36 | 0.79 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 2918 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5FEI · Crystal structure of the bacteriophage phi29 tail knob protein gp9 truncation variant · 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 P04331
- Elsewhere: RCSB PDB 5FEI · PDBe 5FEI · UniProt P04331
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.