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The 2.6 a crystal structure of the lipoxygenase domain of human arachidonate 12-lipoxygenase, 12S-type
Analyse The 2.6 a crystal structure of the lipoxygenase domain of human arachidonate… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3D3L
- Type
- protein
- Length
- 898 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arachidonate 12-lipoxygenase, 12S-type
- EC
- 1.13.11.31
- UniProt
- P18054
- Ligands
- FE
- Pockets
- 7 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 56% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arachidonate 12-lipoxygenase, 12S-type (EC 1.13.11.31) | protein | 451 | 55% helix, 6% strand | P18054 |
| B | Arachidonate 12-lipoxygenase, 12S-type (EC 1.13.11.31) | protein | 447 | 57% helix, 5% strand | P18054 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1146 | 0.81 | 0.83 | 97 | empty |
| 2 | 742 | 0.74 | 0.79 | 69 | empty |
| 3 | 624 | 0.71 | 0.79 | 68 | empty |
| 4 | 51 | 0.65 | 0.95 | 16 | empty |
| 5 | 200 | 0.61 | 0.82 | 33 | empty |
Interfaces
1 interface between chains.
- A–B · 572 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 3D3L · The 2.6 A crystal structure of the lipoxygenase domain of human arachidonate… · the same entry in another collection · chain A against A, TM-score 1.00
- P18054 · AlphaFold monomer V2.0 prediction for polyunsaturated fatty acid lipoxygenase ALOX12… · a predicted model of the same protein · chain B against A, TM-score 0.95
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 P18054
- Elsewhere: RCSB PDB 3D3L · PDBe 3D3L · UniProt P18054
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