MolNFT v1 · #118739 · protein
Crystal structure of the bacteriophage PHI29 tail knob protein GP9 truncation variant
5FB4 · Distal tube protein: “Crystal structure of the bacteriophage PHI29 tail knob protein GP9 truncation variant”. X-ray diffraction, 20 pockets (best druggability 0.65). MolNFT v1 #118739 on GenesisL1: 3D structure, binding sites and…
- 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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