MolNFT v1 · #129234 · protein
Structure of large terminase from the thermophilic bacteriophage D6E in complex with sulfate (crystal form 2)
5OE9 · Large subunit terminase: “Structure of large terminase from the thermophilic bacteriophage D6E in complex with sulfate (crystal form 2)”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.67). MolNFT v1 #129234 on…
- PDB
- 5OE9
- Type
- protein
- Length
- 1,230 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Large subunit terminase
- UniProt
- E5DV50
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Large subunit terminase | protein | 406 | 37% helix, 23% strand | E5DV50 |
| B | Large subunit terminase | protein | 409 | 38% helix, 23% strand | E5DV50 |
| C | Large subunit terminase | protein | 415 | 37% helix, 25% strand | E5DV50 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 687 | 0.67 | 0.76 | 63 | SO4 |
| 2 | 366 | 0.60 | 0.77 | 44 | empty |
| 3 | 322 | 0.60 | 0.78 | 41 | empty |
| 4 | 233 | 0.59 | 0.80 | 29 | SO4 |
| 5 | 294 | 0.56 | 0.77 | 41 | empty |
Interfaces
3 interfaces between chains.
- A–B · 352 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 301 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 212 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5OE9 · Structure of large terminase from the thermophilic bacteriophage D6E in complex with… · 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 E5DV50
- Elsewhere: RCSB PDB 5OE9 · PDBe 5OE9 · UniProt E5DV50
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