Research workbench
Crystal structure of RV0183, a monoglyceride lipase from mycobacterium tuberculosis
Analyse Crystal structure of RV0183, a monoglyceride lipase from mycobacterium… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EIC
- Type
- protein
- Length
- 826 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mycobacterium tuberculosis monoglyceride lipase
- UniProt
- O07427
- Ligands
- SO4, NO3
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 40% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Mycobacterium tuberculosis monoglyceride lipase | protein | 275 | 41% helix, 21% strand | O07427 |
| A | Mycobacterium tuberculosis monoglyceride lipase | protein | 272 | 39% helix, 22% strand | O07427 |
| B | Mycobacterium tuberculosis monoglyceride lipase | protein | 279 | 41% helix, 21% strand | O07427 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains C
- NO3 · Nitrate ion · ion · chains B
- MPD · (4S)-2-methyl-2,4-pentanediol · additive · 3 copies · chains C, A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 344 | 0.72 | 0.84 | 45 | MPD, NO3 |
| 2 | 503 | 0.70 | 0.80 | 67 | SO4, MPD |
| 3 | 635 | 0.69 | 0.77 | 63 | MPD |
| 4 | 550 | 0.61 | 0.74 | 52 | empty |
| 5 | 56 | 0.37 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- C–B · 343 Ų buried · 1 hydrogen bond · protein-protein
- C–A · 290 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 28 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6EIC · Crystal structure of Rv0183, a Monoglyceride Lipase from Mycobacterium Tuberculosis · the same entry in another collection · chain C against C, TM-score 1.00
- O07427 · AlphaFold monomer V2.0 prediction for monoacylglycerol lipase (O07427) · a predicted model of the same protein · chain C against A, TM-score 0.98
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 O07427
- Elsewhere: RCSB PDB 6EIC · PDBe 6EIC · UniProt O07427
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