MolNFT v1 · #73836 · protein
Crystal structure of plic-st, periplasmic lysozyme inhibitor of C-type lysozyme from salmonella typhimurium
3OE3 · Putative periplasmic protein: “Crystal structure of plic-st, periplasmic lysozyme inhibitor of C-type lysozyme from salmonella typhimurium”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.72). MolNFT v1 #73836 on…
- PDB
- 3OE3
- Type
- protein
- Length
- 514 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Putative periplasmic protein
- UniProt
- Q8ZPY8
- Ligands
- NA
- Pockets
- 3 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 2% helix, 65% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Putative periplasmic protein | protein | 85 | 0% helix, 68% strand | Q8ZPY8 |
| B | Putative periplasmic protein | protein | 84 | 0% helix, 68% strand | Q8ZPY8 |
| C, D | Putative periplasmic protein | protein | 88 | 3% helix, 64% strand | Q8ZPY8 |
| E | Putative periplasmic protein | protein | 82 | 4% helix, 63% strand | Q8ZPY8 |
| F | Putative periplasmic protein | protein | 87 | 3% helix, 64% strand | Q8ZPY8 |
Ligands and binding sites
- NA · Sodium ion · metal · 6 copies · chains A, C, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.72 | 0.76 | 73 | empty |
| 2 | 112 | 0.42 | 0.76 | 24 | empty |
| 3 | 124 | 0.40 | 0.75 | 23 | empty |
Interfaces
9 interfaces between chains.
- E–F · 911 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 908 Ų buried · 9 hydrogen bonds · protein-protein
- B–D · 885 Ų buried · 10 hydrogen bonds · protein-protein
- B–E · 315 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 81 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 29 modified, 6 disulfide (engineered, disulfide).
Compared structures
- 3OE3 · Crystal structure of PliC-St, periplasmic lysozyme inhibitor of C-type lysozyme from… · 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 Q8ZPY8
- Elsewhere: RCSB PDB 3OE3 · PDBe 3OE3 · UniProt Q8ZPY8
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