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Crystal structure of Monoglyceride lipase from Bacillus sp. H257 in complex with an 1-myristoyl glycerol analogue
Analyse Crystal structure of Monoglyceride lipase from Bacillus sp. H257 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4KE7
- Type
- protein
- Length
- 487 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.699
- Source
- Bacillus sp.
- Molecule
- Thermostable monoacylglycerol lipase
- EC
- 3.1.1.23
- UniProt
- P82597
- Ligands
- 1QX
- Pockets
- 3 · best druggability 0.69
Structure
x-ray diffraction · resolution 1.699 · 2 distinct chains · 39% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Thermostable monoacylglycerol lipase (EC 3.1.1.23) | protein | 245 | 39% helix, 18% strand | P82597 |
| B | Thermostable monoacylglycerol lipase (EC 3.1.1.23) | protein | 242 | 39% helix, 18% strand | P82597 |
Ligands and binding sites
- 1QX · dodecyl hydrogen (S)-(3-azidopropyl)phosphonate · ligand · 2 copies · chains A, B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 305 | 0.69 | 0.83 | 33 | 1QX |
| 2 | 334 | 0.68 | 0.82 | 35 | 1QX |
| 3 | 167 | 0.42 | 0.74 | 27 | empty |
Interfaces
1 interface between chains.
- A–B · 389 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 4KE7 · Crystal structure of monoglyceride lipase from bacillus sp. H257 in complex with an… · the same entry in another collection · chain A against A, TM-score 1.00
- P82597 · AlphaFold monomer V2.0 prediction for thermostable monoacylglycerol lipase (P82597) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P82597
- Elsewhere: RCSB PDB 4KE7 · PDBe 4KE7 · UniProt P82597
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