Research workbench
Staphylococcus aureus lipase -orlistat complex
Analyse Staphylococcus aureus lipase -orlistat complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KSM
- Type
- protein
- Length
- 764 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase 2
- EC
- 3.1.1.3
- UniProt
- A0A0U1MWF9
- Ligands
- DAO, DH9, BUA, STE, ZN, CA
- Pockets
- 7 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Lipase 2 (EC 3.1.1.3) | protein | 382 | 38% helix, 14% strand | A0A0U1MWF9 |
Ligands and binding sites
- DAO · Lauric acid · ligand · 4 copies · chains A, B
- DH9 · (2S,3S,5S)-5-[(N-formyl-L-leucyl)oxy]-2-hexyl-3-hydroxyhexadecanoic acid · ligand · 2 copies · chains A, B
- BUA · butanoic acid · ligand · 2 copies
- STE · Stearic acid · ligand · chains B
- ZN · Zinc ion · metal · 2 copies · chains A, B
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 481 | 0.71 | 0.80 | 40 | DH9 |
| 2 | 408 | 0.71 | 0.81 | 40 | DH9 |
| 3 | 211 | 0.70 | 0.86 | 29 | empty |
| 4 | 216 | 0.60 | 0.80 | 23 | empty |
| 5 | 205 | 0.59 | 0.81 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 314 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 6KSM · Staphylococcus aureus lipase -Orlistat complex · 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 A0A0U1MWF9
- Elsewhere: RCSB PDB 6KSM · PDBe 6KSM · UniProt A0A0U1MWF9
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