MolNFT v1 · #129235 · protein
Structure of large terminase from the thermophilic bacteriophage D6E in complex with ATP-gamma-S (crystal form 3)
5OEA · Large subunit terminase: “Structure of large terminase from the thermophilic bacteriophage D6E in complex with ATP-gamma-S (crystal…”. X-ray diffraction, 2 ligands (AGS, MG), 19 pockets (best druggability 0.75). MolNFT v1 #129235 on…
- PDB
- 5OEA
- Type
- protein
- Length
- 2,428 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Large subunit terminase
- UniProt
- E5DV50
- Ligands
- AGS, MG
- Pockets
- 19 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Large subunit terminase | protein | 404 | 39% helix, 23% strand | E5DV50 |
| B | Large subunit terminase | protein | 409 | 37% helix, 23% strand | E5DV50 |
| C | Large subunit terminase | protein | 397 | 37% helix, 23% strand | E5DV50 |
| E | Large subunit terminase | protein | 408 | 38% helix, 22% strand | E5DV50 |
| F | Large subunit terminase | protein | 406 | 36% helix, 22% strand | E5DV50 |
Ligands and binding sites
- AGS · Phosphothiophosphoric acid-adenylate ester · ligand · 4 copies · chains A, B, D, E
- MG · Magnesium ion · metal · 4 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 772 | 0.75 | 0.80 | 95 | AGS, MG |
| 2 | 521 | 0.66 | 0.77 | 55 | empty |
| 3 | 569 | 0.66 | 0.76 | 55 | AGS, MG |
| 4 | 514 | 0.65 | 0.77 | 50 | AGS, MG |
| 5 | 331 | 0.63 | 0.79 | 41 | empty |
Interfaces
9 interfaces between chains.
- A–B · 551 Ų buried · 4 hydrogen bonds · protein-protein
- A–F · 442 Ų buried · 7 hydrogen bonds · protein-protein
- B–C · 431 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 361 Ų buried · 4 hydrogen bonds · protein-protein
- A–E · 359 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5OEA · 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 5OEA · PDBe 5OEA · UniProt E5DV50
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