MolNFT v1 · #154552 · protein
Microbial hormone-sensitive lipase- E53 mutant S162A
6KF1: “Microbial hormone-sensitive lipase- E53 mutant S162A”. X-ray diffraction, 3 ligands (NPO, 6NA, SO4), 7 pockets (best druggability 0.82). MolNFT v1 #154552 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KF1
- Type
- protein
- Length
- 1,237 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase
- UniProt
- A0A074MDU6
- Ligands
- NPO, 6NA, SO4
- Pockets
- 7 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Lipase | protein | 309 | 40% helix, 17% strand | A0A074MDU6 |
| D | Lipase | protein | 310 | 39% helix, 16% strand | A0A074MDU6 |
Ligands and binding sites
- NPO · P-nitrophenol · ligand · 11 copies · chains A, B, C, D
- 6NA · Hexanoic acid · ligand · 5 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains C, D
- PGE · Triethylene glycol · additive · chains A, B
- EDO · 1,2-ethanediol · additive · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 659 | 0.82 | 0.86 | 80 | NPO |
| 2 | 826 | 0.81 | 0.83 | 83 | NPO |
| 3 | 491 | 0.77 | 0.85 | 57 | NPO |
| 4 | 480 | 0.77 | 0.84 | 52 | NPO |
| 5 | 55 | 0.33 | 0.77 | 19 | empty |
Interfaces
3 interfaces between chains.
- C–D · 901 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 894 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 639 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6KF1 · Microbial Hormone-sensitive lipase- E53 mutant S162A · 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 6KF1 · PDBe 6KF1 · UniProt A0A074MDU6
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