Research workbench
The structure of the herpes simplex virus DNA-packaging motor PUL15 C- terminal nuclease domain provides insights into cleavage of concatemeric viral genome precursors
Analyse The structure of the herpes simplex virus DNA-packaging motor PUL15 C- terminal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4IOX
- Type
- protein
- Length
- 667 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tripartite terminase subunit UL15; Peptide
- UniProt
- P04295
- Pockets
- 6 · best druggability 0.59
Structure
x-ray diffraction · 4 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tripartite terminase subunit UL15 | protein | 225 | 36% helix, 23% strand | P04295 |
| B | Tripartite terminase subunit UL15 | protein | 216 | 38% helix, 24% strand | P04295 |
| C | Tripartite terminase subunit UL15 | protein | 220 | 38% helix, 23% strand | P04295 |
| D | Peptide | protein | 6 | 0% helix, 17% strand | — |
Ligands and binding sites
- PGE · Triethylene glycol · additive · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
- PG4 · Tetraethylene glycol · additive · chains A
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.59 | 0.76 | 45 | empty |
| 2 | 343 | 0.56 | 0.75 | 42 | empty |
| 3 | 200 | 0.51 | 0.76 | 19 | empty |
| 4 | 123 | 0.46 | 0.77 | 22 | empty |
| 5 | 68 | 0.38 | 0.78 | 14 | empty |
Interfaces
4 interfaces between chains.
- A–C · 507 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 491 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 386 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 354 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 4IOX · The structure of the herpes simplex virus DNA-packaging motor pUL15 C-terminal nuclease… · 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 P04295
- Elsewhere: RCSB PDB 4IOX · PDBe 4IOX · UniProt P04295
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