MolNFT v1 · #189972 · protein
Microbial hormone-sensitive lipase E53 wild type
7W8N: “Microbial hormone-sensitive lipase E53 wild type”. X-ray diffraction, 7 ligands (CCN, 6NA, D8F), 5 pockets (best druggability 0.80). MolNFT v1 #189972 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7W8N
- 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
- CCN, 6NA, D8F, NPO, BUA, NA, SO4
- Pockets
- 5 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Lipase | protein | 309 | 39% helix, 18% strand | A0A074MDU6 |
| C | Lipase | protein | 309 | 39% helix, 18% strand | A0A074MDU6 |
Ligands and binding sites
- CCN · Acetonitrile · ligand · 24 copies · chains A, C, B, D
- 6NA · Hexanoic acid · ligand · 5 copies · chains A, B, C, D
- D8F · (4-nitrophenyl) hexanoate · ligand · 4 copies · chains A, B, C, D
- NPO · P-nitrophenol · ligand · 3 copies · chains B, D
- BUA · butanoic acid · ligand · chains B
- NA · Sodium ion · metal · chains C
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 25 copies · chains A, B, C, D
- DMS · Dimethyl sulfoxide · additive · 13 copies · chains A, B, C, D
- GOL · Glycerol · additive · 9 copies · chains A, B, C, D
- DIO · 1,4-diethylene dioxide · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 731 | 0.80 | 0.84 | 86 | DMS, D8F, GOL, NA |
| 2 | 834 | 0.79 | 0.82 | 85 | CCN, EDO, GOL, D8F |
| 3 | 468 | 0.76 | 0.84 | 57 | GOL, D8F |
| 4 | 479 | 0.75 | 0.83 | 54 | CCN, GOL, D8F |
| 5 | 59 | 0.31 | 0.76 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–B · 899 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 890 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 636 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7W8N · Microbial Hormone-sensitive lipase E53 wild type · 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 7W8N · PDBe 7W8N · UniProt A0A074MDU6
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