Research workbench
Atomic structure of P4 packaging enzyme fitted into a localized reconstruction of bacteriophage PHI6 vertex
Analyse Atomic structure of P4 packaging enzyme fitted into a localized reconstruction… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MUW
- 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
- 16 · best druggability 0.85
Structure
electron microscopy · 4 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, I, K | Packaging enzyme P4 (EC 3.6.1.15) | protein | 269 | 35% helix, 23% strand | P11125 |
| B | Packaging enzyme P4 (EC 3.6.1.15) | protein | 270 | 35% helix, 24% 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
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1137 | 0.85 | 0.85 | 132 | empty |
| 2 | 130 | 0.64 | 0.87 | 28 | CA, ADP |
| 3 | 195 | 0.63 | 0.84 | 35 | CA, ADP |
| 4 | 107 | 0.61 | 0.87 | 21 | CA, ADP |
| 5 | 205 | 0.60 | 0.82 | 39 | CA, ADP |
Interfaces
6 interfaces between chains.
- I–J · 1911 Ų buried · 20 hydrogen bonds · protein-protein
- A–L · 1892 Ų buried · 22 hydrogen bonds · protein-protein
- B–I · 1879 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1872 Ų buried · 26 hydrogen bonds · protein-protein
- J–K · 1855 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5MUW · Atomic structure of P4 packaging enzyme fitted into a localized reconstruction of… · 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 5MUW · PDBe 5MUW · UniProt P11125
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