Research workbench
Anaerobic crystal structure of DELTA413-417:GS lox in complex with arachidonate
Analyse Anaerobic crystal structure of DELTA413-417:GS lox in complex with arachidonate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QWT
- Type
- protein
- Length
- 2,725 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 0.86
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Allene oxide synthase-lipoxygenase protein (EC 1.13.11.40) | protein | 681 | 44% helix, 14% strand | O16025 |
| B | Allene oxide synthase-lipoxygenase protein (EC 1.13.11.40) | protein | 679 | 43% helix, 14% strand | O16025 |
| C | Allene oxide synthase-lipoxygenase protein (EC 1.13.11.40) | protein | 684 | 43% helix, 15% strand | O16025 |
| D | Allene oxide synthase-lipoxygenase protein (EC 1.13.11.40) | protein | 681 | 43% helix, 14% strand | O16025 |
Ligands and binding sites
- ACD · Arachidonic acid · ligand · chains C
- 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 · 6 copies · chains A, B, C, D
- ACT · Acetate ion · additive · 25 copies · chains A, B, C, D
- GOL · Glycerol · additive · 17 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 | 994 | 0.86 | 0.88 | 125 | CA, GOL |
| 2 | 1046 | 0.86 | 0.87 | 137 | GOL, ACT |
| 3 | 803 | 0.82 | 0.84 | 110 | ACT, ACD |
| 4 | 135 | 0.81 | 0.98 | 37 | ACT |
| 5 | 155 | 0.80 | 0.96 | 32 | empty |
Interfaces
6 interfaces between chains.
- C–D · 1444 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1441 Ų buried · 14 hydrogen bonds · protein-protein
- B–C · 549 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 534 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 378 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4QWT · Anaerobic crystal structure of delta413-417:GS LOX in complex with arachidonate · the same entry in another collection · chain D against D, 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 4QWT · PDBe 4QWT · UniProt O16025
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