Research workbench
Structure of large terminase from the thermophilic bacteriophage D6E in complex with sulfate (crystal form 2)
Analyse Structure of large terminase from the thermophilic bacteriophage D6E in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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