MolNFT v1 · #110406 · protein
Crystal structure of the small terminase from thermophilic phage G20C
4XVN: “Crystal structure of the small terminase from thermophilic phage G20C”. X-ray diffraction, 16 pockets (best druggability 0.64). MolNFT v1 #110406 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4XVN
- Type
- protein
- Length
- 795 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Small terminase
- Pockets
- 16 · best druggability 0.64
Structure
x-ray diffraction · 6 distinct chains · 75% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small terminase | protein | 130 | 75% helix, 2% strand | — |
| B | Small terminase | protein | 123 | 78% helix, 2% strand | — |
| C | Small terminase | protein | 129 | 75% helix, 2% strand | — |
| D | Small terminase | protein | 139 | 74% helix, 1% strand | — |
| E | Small terminase | protein | 137 | 72% helix, 0% strand | — |
| F | Small terminase | protein | 137 | 74% helix, 1% strand | — |
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 | 658 | 0.64 | 0.74 | 51 | empty |
| 2 | 199 | 0.57 | 0.80 | 26 | empty |
| 3 | 67 | 0.55 | 0.87 | 14 | empty |
| 4 | 92 | 0.52 | 0.84 | 16 | empty |
| 5 | 165 | 0.52 | 0.79 | 21 | empty |
Interfaces
9 interfaces between chains.
- D–E · 1821 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 1718 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 1599 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1543 Ų buried · 10 hydrogen bonds · protein-protein
- C–F · 248 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 modified (engineered).
Compared structures
- 4XVN · Crystal structure of the small terminase from thermophilic phage G20C · 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
- Elsewhere: RCSB PDB 4XVN · PDBe 4XVN
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