MolNFT v1 · #127379 · protein
Atomic structure fitted into a localized reconstruction of bacteriophage PHI6 packaging hexamer P4
5MUV · Packaging enzyme P4: “Atomic structure fitted into a localized reconstruction of bacteriophage PHI6 packaging hexamer P4”. Electron microscopy, 2 ligands (ADP, CA), 18 pockets (best druggability 0.84). MolNFT v1 #127379 on…
- PDB
- 5MUV
- Type
- protein
- Length
- 1,621 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Packaging enzyme P4
- EC
- 3.6.1.15
- UniProt
- P11125
- Ligands
- ADP, CA
- Pockets
- 18 · best druggability 0.84
Structure
electron microscopy · 4 distinct chains · 35% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I, K | Packaging enzyme P4 (EC 3.6.1.15) | protein | 269 | 35% helix, 22% strand | P11125 |
| B | Packaging enzyme P4 (EC 3.6.1.15) | protein | 270 | 35% helix, 23% strand | P11125 |
| J | Packaging enzyme P4 (EC 3.6.1.15) | protein | 269 | 35% helix, 23% strand | P11125 |
| L | Packaging enzyme P4 (EC 3.6.1.15) | protein | 275 | 35% helix, 21% strand | P11125 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 6 copies · chains A, L, B, I, J, K
- CA · Calcium ion · metal · 6 copies · chains A, B, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1161 | 0.84 | 0.85 | 136 | empty |
| 2 | 177 | 0.64 | 0.85 | 36 | CA, ADP |
| 3 | 132 | 0.63 | 0.87 | 30 | CA, ADP |
| 4 | 184 | 0.62 | 0.83 | 43 | CA, ADP |
| 5 | 173 | 0.61 | 0.84 | 38 | CA |
Interfaces
6 interfaces between chains.
- I–J · 1899 Ų buried · 20 hydrogen bonds · protein-protein
- A–L · 1894 Ų buried · 22 hydrogen bonds · protein-protein
- B–I · 1873 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1872 Ų buried · 26 hydrogen bonds · protein-protein
- K–L · 1860 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 5MUV · Atomic structure fitted into a localized reconstruction of bacteriophage phi6 packaging… · 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 P11125
- Elsewhere: RCSB PDB 5MUV · PDBe 5MUV · UniProt P11125
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