Research workbench
Crystal structure hormone-sensitive lipase from a metagenome library
Analyse Crystal structure hormone-sensitive lipase from a metagenome library in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DNM
- Type
- protein
- Length
- 1,175 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ESTERASE/LIPASE
- EC
- 3.1.1.-
- UniProt
- Q0GMU1
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ESTERASE/LIPASE (EC 3.1.1.-) | protein | 297 | 42% helix, 18% strand | Q0GMU1 |
| B | ESTERASE/LIPASE (EC 3.1.1.-) | protein | 296 | 43% helix, 15% strand | Q0GMU1 |
| C | ESTERASE/LIPASE (EC 3.1.1.-) | protein | 291 | 43% helix, 19% strand | Q0GMU1 |
| D | ESTERASE/LIPASE (EC 3.1.1.-) | protein | 291 | 42% helix, 19% strand | Q0GMU1 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 14 copies · chains A, B, C, D
- BME · Beta-mercaptoethanol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.77 | 0.83 | 42 | BME |
| 2 | 498 | 0.77 | 0.84 | 40 | BME |
| 3 | 538 | 0.72 | 0.80 | 39 | BME |
| 4 | 500 | 0.71 | 0.80 | 42 | BME |
| 5 | 237 | 0.58 | 0.79 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–B · 937 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 931 Ų buried · 15 hydrogen bonds · protein-protein
- B–C · 282 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 3DNM · Crystal Structure Hormone-Sensitive Lipase from a Metagenome Library · 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 Q0GMU1
- Elsewhere: RCSB PDB 3DNM · PDBe 3DNM · UniProt Q0GMU1
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