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
- 5FB4
- Type
- protein
- Length
- 1,542 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Distal tube protein
- UniProt
- P04331
- Pockets
- 20 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 16% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Distal tube protein | protein | 511 | 17% helix, 37% strand | P04331 |
| B | Distal tube protein | protein | 515 | 16% helix, 37% strand | P04331 |
| C | Distal tube protein | protein | 516 | 16% helix, 36% strand | P04331 |
Ligands and binding sites
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 193 | 0.65 | 0.85 | 38 | empty |
| 2 | 327 | 0.64 | 0.80 | 41 | empty |
| 3 | 316 | 0.63 | 0.79 | 36 | empty |
| 4 | 179 | 0.62 | 0.84 | 41 | empty |
| 5 | 153 | 0.60 | 0.84 | 26 | empty |
Interfaces
2 interfaces between chains.
- A–B · 3139 Ų buried · 35 hydrogen bonds · protein-protein
- B–C · 3113 Ų buried · 35 hydrogen bonds · protein-protein
Compared structures
- 5FB4 · 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 5FB4 · PDBe 5FB4 · UniProt P04331
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