MolNFT v1 · #102387 · protein
Structure of bacteriophage SPN1S endolysin from salmonella typhimurium
4OK7: “Structure of bacteriophage SPN1S endolysin from salmonella typhimurium”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.56). MolNFT v1 #102387 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4OK7
- Type
- protein
- Length
- 669 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endolysin
- UniProt
- H2D0G4
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.56
Structure
x-ray diffraction · 1 distinct chain · 57% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Endolysin | protein | 223 | 57% helix, 2% strand | H2D0G4 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C
- GOL · Glycerol · additive · 4 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 191 | 0.56 | 0.80 | 30 | SO4 |
| 2 | 225 | 0.51 | 0.76 | 37 | empty |
| 3 | 87 | 0.48 | 0.82 | 20 | empty |
| 4 | 79 | 0.47 | 0.82 | 22 | empty |
| 5 | 88 | 0.37 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1128 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 933 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 903 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4OK7 · Structure of bacteriophage SPN1S endolysin from Salmonella typhimurium · 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 H2D0G4
- Elsewhere: RCSB PDB 4OK7 · PDBe 4OK7 · UniProt H2D0G4
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