Research workbench
Crystal structure of monoglyceride lipase from bacillus sp. H257 in complex with an 1-stearyol 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
- 4KE9
- Type
- protein
- Length
- 987 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Thermostable monoacylglycerol lipase
- EC
- 3.1.1.23
- UniProt
- P82597
- Ligands
- 1R1
- Pockets
- 12 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, D | Thermostable monoacylglycerol lipase (EC 3.1.1.23) | protein | 247 | 36% helix, 19% strand | P82597 |
| C | Thermostable monoacylglycerol lipase (EC 3.1.1.23) | protein | 246 | 38% helix, 17% strand | P82597 |
Ligands and binding sites
- 1R1 · hexadecyl hydrogen (R)-(3-azidopropyl)phosphonate · ligand · 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, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.81 | 0.93 | 41 | 1R1 |
| 2 | 266 | 0.78 | 0.90 | 45 | 1R1 |
| 3 | 348 | 0.74 | 0.85 | 41 | 1R1 |
| 4 | 315 | 0.72 | 0.84 | 39 | 1R1 |
| 5 | 498 | 0.67 | 0.78 | 38 | empty |
Interfaces
5 interfaces between chains.
- A–C · 745 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 689 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 403 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 250 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 246 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent (covalent ligand).
Compared structures
- 4KE9 · 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 C 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 4KE9 · PDBe 4KE9 · UniProt P82597
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