Research workbench
Catalytic domain of the antimicrobial peptidase lysostaphin from staphylococcus simulans crystallized in the presence of phosphate
Analyse Catalytic domain of the antimicrobial peptidase lysostaphin from staphylococcus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QP5
- Type
- protein
- Length
- 267 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lysostaphin
- EC
- 3.4.24.75
- UniProt
- P10547
- Ligands
- ZN, PO4
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Lysostaphin (EC 3.4.24.75) | protein | 134 | 10% helix, 41% strand | P10547 |
| B | Lysostaphin (EC 3.4.24.75) | protein | 133 | 9% helix, 44% strand | P10547 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 152 | 0.60 | 0.83 | 27 | PO4, GOL |
| 2 | 179 | 0.57 | 0.81 | 30 | PO4, GOL |
Interfaces
1 interface between chains.
- A–B · 101 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4QP5 · Catalytic domain of the antimicrobial peptidase lysostaphin from Staphylococcus simulans… · the same entry in another collection · chain A against A, TM-score 1.00
- P10547 · AlphaFold monomer V2.0 prediction for lysostaphin (P10547) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P10547
- Elsewhere: RCSB PDB 4QP5 · PDBe 4QP5 · UniProt P10547
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