MolNFT v1 · #112835 · protein
Crystal structure of a soluble variant of monoglyceride lipase from saccharomyces cerevisiae in complex with a substrate analog
4ZXF: “Crystal structure of a soluble variant of monoglyceride lipase from saccharomyces cerevisiae in complex with…”. X-ray diffraction, 3 ligands (4S7, SO4, NO3), 15 pockets (best druggability 0.85). MolNFT v1 #112835 on GenesisL1: 3D…
- PDB
- 4ZXF
- Type
- protein
- Length
- 1,215 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoglyceride lipase
- EC
- 3.1.1.23
- UniProt
- P28321
- Ligands
- 4S7, SO4, NO3
- Pockets
- 15 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 40% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Monoglyceride lipase (EC 3.1.1.23) | protein | 308 | 41% helix, 18% strand | P28321 |
| B | Monoglyceride lipase (EC 3.1.1.23) | protein | 307 | 40% helix, 19% strand | P28321 |
| C | Monoglyceride lipase (EC 3.1.1.23) | protein | 307 | 42% helix, 18% strand | P28321 |
| D | Monoglyceride lipase (EC 3.1.1.23) | protein | 293 | 39% helix, 17% strand | P28321 |
Ligands and binding sites
- 4S7 · 1-{3-[(R)-hydroxy(octadecyloxy)phosphoryl]propyl}triaza-1,2-dien-2-ium · ligand · chains C, D
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- NO3 · Nitrate ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 712 | 0.85 | 0.88 | 75 | 4S7 |
| 2 | 232 | 0.83 | 0.96 | 35 | empty |
| 3 | 228 | 0.83 | 0.95 | 38 | empty |
| 4 | 210 | 0.81 | 0.94 | 33 | empty |
| 5 | 476 | 0.72 | 0.81 | 51 | empty |
Interfaces
5 interfaces between chains.
- C–D · 792 Ų buried · 5 hydrogen bonds · protein-protein
- B–D · 719 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 627 Ų buried · 9 hydrogen bonds · protein-protein
- A–B · 311 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 251 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4ZXF · Crystal Structure of a Soluble Variant of Monoglyceride Lipase from Saccharomyces… · the same entry in another collection · chain B against B, TM-score 1.00
- P28321 · AlphaFold monomer V2.0 prediction for monoglyceride lipase (P28321) · a predicted model of the same protein · chain B 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 P28321
- Elsewhere: RCSB PDB 4ZXF · PDBe 4ZXF · UniProt P28321
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