Research workbench
Ether lipid-generating enzyme agps in complex with inhibitor ZINC69435460
Analyse Ether lipid-generating enzyme agps in complex with inhibitor ZINC69435460 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AE1
- Type
- protein
- Length
- 2,222 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alkyldihydroxyacetonephosphate synthase, peroxisomal
- EC
- 2.5.1.26
- UniProt
- P97275
- Ligands
- B2Z, 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 (EC 2.5.1.26) | protein | 560 | 36% helix, 21% strand | P97275 |
| B | Alkyldihydroxyacetonephosphate synthase, peroxisomal (EC 2.5.1.26) | protein | 539 | 37% helix, 22% strand | P97275 |
| C | Alkyldihydroxyacetonephosphate synthase, peroxisomal (EC 2.5.1.26) | protein | 559 | 36% helix, 21% strand | P97275 |
| D | Alkyldihydroxyacetonephosphate synthase, peroxisomal (EC 2.5.1.26) | protein | 564 | 37% helix, 21% strand | P97275 |
Ligands and binding sites
- B2Z · (3-(2-fluorophenyl)-N-(1-(2-oxo-2,3-dihydro-1H-benzo[d]imidazol-5-yl)ethyl)butanamide) · 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, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 941 | 0.90 | 0.93 | 107 | B2Z, FAD |
| 2 | 900 | 0.90 | 0.93 | 104 | B2Z, FAD |
| 3 | 956 | 0.90 | 0.91 | 102 | B2Z, FAD |
| 4 | 1149 | 0.88 | 0.89 | 137 | B2Z, FAD |
| 5 | 1000 | 0.84 | 0.85 | 96 | SO4 |
Interfaces
4 interfaces between chains.
- C–D · 3431 Ų buried · 46 hydrogen bonds · protein-protein
- A–B · 3384 Ų buried · 49 hydrogen bonds · protein-protein
- A–D · 599 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 332 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 5AE1 · Ether Lipid-Generating Enzyme AGPS in complex with inhibitor ZINC69435460 · the same entry in another collection · chain A against A, TM-score 1.00
- P97275 · AlphaFold monomer V2.0 prediction for alkyldihydroxyacetonephosphate synthase… · 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 P97275
- Elsewhere: RCSB PDB 5AE1 · PDBe 5AE1 · UniProt P97275
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