MolNFT v1 · #154976 · protein
Staphylococcus aureus lipase - native
6KSI · Lipase 2: “Staphylococcus aureus lipase - native”. X-ray diffraction, 8 ligands (DAO, 6NA, LEA), 7 pockets (best druggability 0.72). MolNFT v1 #154976 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KSI
- 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, 6NA, LEA, OCA, BUA, PLM, ZN, CA
- Pockets
- 7 · best druggability 0.72
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 · 3 copies · chains A, B
- 6NA · Hexanoic acid · ligand · 2 copies · chains A, B
- LEA · Pentanoic acid · ligand · 2 copies · chains A, B
- OCA · Octanoic acid (caprylic acid) · ligand · 2 copies · chains A, B
- BUA · butanoic acid · ligand · 2 copies · chains A, B
- PLM · Palmitic acid · ligand · chains A
- 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 464 | 0.72 | 0.81 | 43 | 6NA, LEA, OCA, BUA |
| 2 | 489 | 0.70 | 0.79 | 40 | 6NA, LEA, OCA, BUA |
| 3 | 144 | 0.69 | 0.89 | 26 | empty |
| 4 | 223 | 0.61 | 0.81 | 25 | empty |
| 5 | 213 | 0.60 | 0.81 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 358 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6KSI · Staphylococcus aureus lipase - native · 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 6KSI · PDBe 6KSI · UniProt A0A0U1MWF9
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