Research workbench
Structure of P22 large terminase nuclease domain
Analyse Structure of P22 large terminase nuclease domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DKW
- Type
- protein
- Length
- 776 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Large terminase protein
- UniProt
- P26745
- Ligands
- MG, SO4
- Pockets
- 12 · best druggability 0.73
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Large terminase protein | protein | 194 | 35% helix, 23% strand | P26745 |
Ligands and binding sites
- MG · Magnesium ion · metal · 8 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 851 | 0.73 | 0.78 | 78 | empty |
| 2 | 282 | 0.52 | 0.75 | 37 | MG |
| 3 | 108 | 0.48 | 0.80 | 22 | empty |
| 4 | 183 | 0.45 | 0.75 | 23 | MG |
| 5 | 174 | 0.45 | 0.75 | 25 | MG |
Interfaces
4 interfaces between chains.
- A–C · 585 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 581 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 390 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 320 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4DKW · Structure of P22 Large terminase nuclease domain · 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 P26745
- Elsewhere: RCSB PDB 4DKW · PDBe 4DKW · UniProt P26745
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