Research workbench
Crystal structure of secreted inactive form of P1 phage endolysin lyz
Analyse Crystal structure of secreted inactive form of P1 phage endolysin lyz in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1XJU
- Type
- protein
- Length
- 311 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysozyme
- EC
- 3.2.1.17
- UniProt
- Q37875
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysozyme (EC 3.2.1.17) | protein | 156 | 60% helix, 8% strand | Q37875 |
| B | Lysozyme (EC 3.2.1.17) | protein | 155 | 61% helix, 8% strand | Q37875 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 131 | 0.52 | 0.80 | 20 | empty |
| 2 | 195 | 0.46 | 0.74 | 35 | empty |
| 3 | 105 | 0.45 | 0.79 | 22 | empty |
| 4 | 101 | 0.37 | 0.75 | 19 | empty |
| 5 | 79 | 0.36 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 473 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 1XJU · Crystal structure of secreted inactive form of P1 phage endolysin Lyz · 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 Q37875
- Elsewhere: RCSB PDB 1XJU · PDBe 1XJU · UniProt Q37875
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