Research workbench
An atomic view of the nonameric small terminase subunit of bacteriophage P22
Analyse An atomic view of the nonameric small terminase subunit of bacteriophage P22 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P9A
- Type
- protein
- Length
- 1,202 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA-packaging protein GP3
- UniProt
- P04893
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 5 distinct chains · 49% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA-packaging protein GP3 | protein | 139 | 49% helix, 17% strand | P04893 |
| B, E, H, I | DNA-packaging protein GP3 | protein | 132 | 50% helix, 17% strand | P04893 |
| C, G | DNA-packaging protein GP3 | protein | 133 | 51% helix, 19% strand | P04893 |
| D | DNA-packaging protein GP3 | protein | 135 | 48% helix, 19% strand | P04893 |
| F | DNA-packaging protein GP3 | protein | 134 | 48% helix, 19% strand | P04893 |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 59 | 0.70 | 0.96 | 21 | empty |
| 2 | 51 | 0.68 | 0.97 | 16 | empty |
| 3 | 51 | 0.68 | 0.97 | 19 | empty |
| 4 | 320 | 0.68 | 0.82 | 35 | empty |
| 5 | 283 | 0.67 | 0.83 | 39 | empty |
Interfaces
18 interfaces between chains.
- C–D · 2101 Ų buried · 23 hydrogen bonds · protein-protein
- A–I · 2090 Ų buried · 20 hydrogen bonds · protein-protein
- H–I · 2074 Ų buried · 17 hydrogen bonds · protein-protein
- G–H · 2028 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2017 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 3P9A · An atomic view of the nonameric small terminase subunit of Bacteriophage P22 · 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 P04893
- Elsewhere: RCSB PDB 3P9A · PDBe 3P9A · UniProt P04893
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