MolNFT v1 · #154555 · protein
Microbial hormone-sensitive lipase E53 mutant I256L
6KF5: “Microbial hormone-sensitive lipase E53 mutant I256L”. X-ray diffraction, 3 ligands (D8F, 6NA, 2FK), 6 pockets (best druggability 0.80). MolNFT v1 #154555 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KF5
- Type
- protein
- Length
- 1,235 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Lipase
- UniProt
- A0A074MDU6
- Ligands
- D8F, 6NA, 2FK
- Pockets
- 6 · best druggability 0.80
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 | 41% helix, 18% strand | A0A074MDU6 |
| D | Lipase | protein | 308 | 40% helix, 17% strand | A0A074MDU6 |
Ligands and binding sites
- D8F · (4-nitrophenyl) hexanoate · ligand · 4 copies · chains A, B, C, D
- 6NA · Hexanoic acid · ligand · chains A
- 2FK · Superoxo ion · ligand · chains A
- GOL · Glycerol · additive · 8 copies · chains A, B, D, C
- EDO · 1,2-ethanediol · additive · 3 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 719 | 0.80 | 0.84 | 88 | EDO, D8F |
| 2 | 842 | 0.79 | 0.82 | 91 | D8F, 2FK |
| 3 | 485 | 0.76 | 0.83 | 56 | D8F, GOL |
| 4 | 445 | 0.75 | 0.84 | 55 | D8F, GOL |
| 5 | 51 | 0.29 | 0.76 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 962 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 944 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 658 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6KF5 · Microbial Hormone-sensitive lipase E53 mutant I256L · 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 6KF5 · PDBe 6KF5 · UniProt A0A074MDU6
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