Research workbench
P4 protein from bacteriophage PHI6 in complex with ADP
Analyse P4 protein from bacteriophage PHI6 in complex with ADP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BLO
- Type
- protein
- Length
- 3,236 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Packaging enzyme P4
- EC
- 3.6.1.15
- UniProt
- P11125
- Ligands
- ADP, CA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 5 distinct chains · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, H, I, K | Packaging enzyme P4 (EC 3.6.1.15) | protein | 269 | 35% helix, 23% strand | P11125 |
| B, C, D | Packaging enzyme P4 (EC 3.6.1.15) | protein | 270 | 35% helix, 24% strand | P11125 |
| E, F, J | Packaging enzyme P4 (EC 3.6.1.15) | protein | 269 | 35% helix, 23% strand | P11125 |
| G | Packaging enzyme P4 (EC 3.6.1.15) | protein | 268 | 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 · 12 copies · chains A, L, B, C, H, D, E, F, G, I, J, K
- CA · Calcium ion · metal · 12 copies · chains A, B, C, D, E, F, G, H, I, J, K, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1029 | 0.85 | 0.86 | 130 | empty |
| 2 | 1082 | 0.84 | 0.85 | 133 | empty |
| 3 | 554 | 0.70 | 0.79 | 72 | CA, ADP |
| 4 | 298 | 0.63 | 0.80 | 45 | CA, ADP |
| 5 | 119 | 0.63 | 0.88 | 28 | CA, ADP |
Interfaces
14 interfaces between chains.
- I–J · 1909 Ų buried · 20 hydrogen bonds · protein-protein
- A–L · 1904 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 1892 Ų buried · 26 hydrogen bonds · protein-protein
- B–I · 1879 Ų buried · 23 hydrogen bonds · protein-protein
- C–H · 1878 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 4BLO · P4 protein from bacteriophage PHI6 in complex with ADP · 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 4BLO · PDBe 4BLO · UniProt P11125
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