Research workbench
Crystal structure of DELTA413-417:GS I805A lox
Analyse Crystal structure of DELTA413-417:GS I805A lox in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3FG4
- Type
- protein
- Length
- 2,717 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Allene oxide synthase-lipoxygenase protein
- EC
- 1.13.11.40
- UniProt
- O16025
- Ligands
- ACD, CA, FE2, CL
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 43% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Allene oxide synthase-lipoxygenase protein (EC 1.13.11.40) | protein | 682 | 43% helix, 14% strand | O16025 |
| B | Allene oxide synthase-lipoxygenase protein (EC 1.13.11.40) | protein | 676 | 43% helix, 14% strand | O16025 |
| C | Allene oxide synthase-lipoxygenase protein (EC 1.13.11.40) | protein | 681 | 43% helix, 15% strand | O16025 |
| D | Allene oxide synthase-lipoxygenase protein (EC 1.13.11.40) | protein | 678 | 44% helix, 14% strand | O16025 |
Ligands and binding sites
- ACD · Arachidonic acid · ligand · 4 copies · chains A, B, C, D
- CA · Calcium ion · metal · 8 copies · chains A, B, C, D
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
- CL · Chloride ion · ion · 4 copies · chains A, B, C, D
- ACY · Acetic acid · additive · 21 copies · chains A, B, C, D
- GOL · Glycerol · additive · 19 copies · chains A, D, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 995 | 0.87 | 0.89 | 141 | GOL |
| 2 | 1099 | 0.87 | 0.88 | 160 | CA, GOL |
| 3 | 140 | 0.79 | 0.96 | 33 | empty |
| 4 | 143 | 0.78 | 0.96 | 33 | empty |
| 5 | 323 | 0.77 | 0.88 | 46 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1425 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 1370 Ų buried · 12 hydrogen bonds · protein-protein
- B–C · 551 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 548 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 381 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 3FG4 · Crystal structure of Delta413-417:GS I805A LOX · the same entry in another collection · chain A against A, TM-score 1.00
- O16025 · AlphaFold monomer V2.0 prediction for allene oxide synthase- lipoxygenase protein (O16025) · a predicted model of the same protein · chain C 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 O16025
- Elsewhere: RCSB PDB 3FG4 · PDBe 3FG4 · UniProt O16025
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