MolNFT v1 · #154556 · protein
Microbial hormone-sensitive lipase E53 mutant S285G
6KF7: “Microbial hormone-sensitive lipase E53 mutant S285G”. X-ray diffraction, 4 ligands (D8F, 6NA, NPO), 9 pockets (best druggability 0.78). MolNFT v1 #154556 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KF7
- Type
- protein
- Length
- 1,236 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase
- UniProt
- A0A074MDU6
- Ligands
- D8F, 6NA, NPO, SO4
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 1 distinct chain · 41% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Lipase | protein | 309 | 41% helix, 17% strand | A0A074MDU6 |
Ligands and binding sites
- D8F · (4-nitrophenyl) hexanoate · ligand · 4 copies · chains A, B, C, D
- 6NA · Hexanoic acid · ligand · 2 copies · chains A, C
- NPO · P-nitrophenol · ligand · chains D
- SO4 · Sulfate ion · ion · 2 copies · chains A, D
- GOL · Glycerol · additive · 16 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 13 copies · chains A, B, C, D
- PGE · Triethylene glycol · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 549 | 0.78 | 0.84 | 66 | D8F, GOL |
| 2 | 618 | 0.76 | 0.82 | 70 | 6NA, D8F |
| 3 | 733 | 0.76 | 0.81 | 75 | D8F, SO4 |
| 4 | 137 | 0.76 | 0.94 | 26 | D8F, GOL |
| 5 | 140 | 0.74 | 0.93 | 25 | D8F, GOL |
Interfaces
3 interfaces between chains.
- A–B · 948 Ų buried · 15 hydrogen bonds · protein-protein
- C–D · 935 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 661 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 6KF7 · Microbial Hormone-sensitive lipase E53 mutant S285G · 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 A0A074MDU6
- Elsewhere: RCSB PDB 6KF7 · PDBe 6KF7 · UniProt A0A074MDU6
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