MolNFT v1 · #74868 · protein
An atomic view of the nonameric small terminase subunit of bacteriophage P22
3P9A · DNA-packaging protein GP3: “An atomic view of the nonameric small terminase subunit of bacteriophage P22”. X-ray diffraction, 20 pockets (best druggability 0.70). MolNFT v1 #74868 on GenesisL1: 3D structure, binding sites and…
- 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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