Research workbench
Ether lipid-generating enzyme agps in complex with antimycin a
Analyse Ether lipid-generating enzyme agps in complex with antimycin a in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5AE3
- Type
- protein
- Length
- 2,176 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
- AWB, FAD, SO4
- Pockets
- 20 · best druggability 0.89
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 | 539 | 36% helix, 21% strand | P97275 |
| B | Alkyldihydroxyacetonephosphate synthase, peroxisomal (EC 2.5.1.26) | protein | 539 | 36% helix, 22% strand | P97275 |
| C | Alkyldihydroxyacetonephosphate synthase, peroxisomal (EC 2.5.1.26) | protein | 551 | 36% helix, 21% strand | P97275 |
| D | Alkyldihydroxyacetonephosphate synthase, peroxisomal (EC 2.5.1.26) | protein | 547 | 36% helix, 21% strand | P97275 |
Ligands and binding sites
- AWB · [(2R,3S,6S,7R,8R)-3-[(3-formamido-2-oxidanyl-phenyl)carbonylamino]-8-hexyl-2,6-dimethyl-4,9-bis(oxidanylidene)-1,5-dioxonan-7-yl] 3-methylbutanoate · ligand · 4 copies · chains A, B, C, D
- FAD · Flavin-adenine dinucleotide · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 3 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 | 1057 | 0.89 | 0.90 | 106 | AWB, FAD |
| 2 | 1067 | 0.89 | 0.90 | 115 | AWB, FAD |
| 3 | 1132 | 0.88 | 0.89 | 124 | AWB, FAD |
| 4 | 1161 | 0.87 | 0.88 | 118 | AWB, FAD |
| 5 | 720 | 0.83 | 0.87 | 87 | SO4 |
Interfaces
4 interfaces between chains.
- C–D · 3400 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 3356 Ų buried · 51 hydrogen bonds · protein-protein
- A–D · 426 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 384 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5AE3 · Ether Lipid-Generating Enzyme AGPS in complex with antimycin A · 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 A 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 5AE3 · PDBe 5AE3 · UniProt P97275
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