MolNFT v1 · #104916 · protein
Catalytic domain of the antimicrobial peptidase lysostaphin from staphylococcus simulans crystallized in the presence of phosphate
4QP5: “Catalytic domain of the antimicrobial peptidase lysostaphin from staphylococcus simulans crystallized in the…”. X-ray diffraction, 2 ligands (ZN, PO4), 2 pockets (best druggability 0.60). MolNFT v1 #104916 on GenesisL1: 3D…
- 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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