MolNFT v1 · #113393 · protein
Ether lipid-generating enzyme agps in complex with inhibitor 1E
5AE2 · Alkyldihydroxyacetonephosphate synthase, peroxisomal: “Ether lipid-generating enzyme agps in complex with inhibitor 1E”. X-ray diffraction, 3 ligands (FYC, FAD, SO4), 20 pockets (best druggability 0.90). MolNFT v1 #113393 on…
- PDB
- 5AE2
- Type
- protein
- Length
- 2,210 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkyldihydroxyacetonephosphate synthase, peroxisomal
- UniProt
- P97275
- Ligands
- FYC, FAD, SO4
- Pockets
- 20 · best druggability 0.90
Structure
x-ray diffraction · 4 distinct chains · 36% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Alkyldihydroxyacetonephosphate synthase, peroxisomal | protein | 561 | 35% helix, 21% strand | P97275 |
| B | Alkyldihydroxyacetonephosphate synthase, peroxisomal | protein | 542 | 36% helix, 22% strand | P97275 |
| C | Alkyldihydroxyacetonephosphate synthase, peroxisomal | protein | 557 | 36% helix, 21% strand | P97275 |
| D | Alkyldihydroxyacetonephosphate synthase, peroxisomal | protein | 550 | 36% helix, 21% strand | P97275 |
Ligands and binding sites
- FYC · 3-(2-fluorophenyl)-2-methyl-N-((2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)methyl)acrylamide · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 973 | 0.90 | 0.92 | 113 | FYC, FAD |
| 2 | 864 | 0.90 | 0.93 | 93 | FYC, FAD |
| 3 | 1160 | 0.89 | 0.91 | 131 | FYC, FAD |
| 4 | 994 | 0.89 | 0.90 | 105 | FYC, FAD |
| 5 | 872 | 0.84 | 0.87 | 107 | SO4 |
Interfaces
4 interfaces between chains.
- C–D · 3430 Ų buried · 52 hydrogen bonds · protein-protein
- A–B · 3363 Ų buried · 54 hydrogen bonds · protein-protein
- A–D · 731 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 471 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5AE2 · Ether Lipid-Generating Enzyme AGPS in complex with inhibitor 1e · the same entry in another collection · chain D against D, TM-score 1.00
- P97275 · AlphaFold monomer V2.0 prediction for alkyldihydroxyacetonephosphate synthase… · a predicted model of the same protein · chain D 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 P97275
- Elsewhere: RCSB PDB 5AE2 · PDBe 5AE2 · UniProt P97275
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