Research workbench
Crystal structure of salmonella typhimurium plig, a periplasmic lysozyme inhibitor of G-type lysozyme
Analyse Crystal structure of salmonella typhimurium plig, a periplasmic lysozyme… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DY5
- Type
- protein
- Length
- 325 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Gifsy-1 prophage protein
- UniProt
- Q8ZMZ1
- Ligands
- CL
- Pockets
- 3 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Gifsy-1 prophage protein | protein | 111 | 4% helix, 50% strand | Q8ZMZ1 |
| B | Gifsy-1 prophage protein | protein | 107 | 4% helix, 51% strand | Q8ZMZ1 |
| C | Gifsy-1 prophage protein | protein | 107 | 4% helix, 51% strand | Q8ZMZ1 |
Ligands and binding sites
- CL · Chloride ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 439 | 0.68 | 0.80 | 44 | GOL |
| 2 | 67 | 0.54 | 0.87 | 19 | empty |
| 3 | 52 | 0.26 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 635 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 615 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 38 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4DY5 · Crystal structure of Salmonella Typhimurium PliG, a periplasmic lysozyme inhibitor of… · 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 Q8ZMZ1
- Elsewhere: RCSB PDB 4DY5 · PDBe 4DY5 · UniProt Q8ZMZ1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.