Research workbench
Cyanothece lipoxygenase 2 (CSPLOX2)
Analyse Cyanothece lipoxygenase 2 (CSPLOX2) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MED
- Type
- protein
- Length
- 1,134 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arachidonate 15-lipoxygenase
- EC
- 1.13.11.33
- UniProt
- B7JX99
- Ligands
- FE
- Pockets
- 16 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arachidonate 15-lipoxygenase (EC 1.13.11.33) | protein | 569 | 52% helix, 9% strand | B7JX99 |
| B | Arachidonate 15-lipoxygenase (EC 1.13.11.33) | protein | 565 | 53% helix, 9% strand | B7JX99 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- PGR · R-1,2-propanediol · additive · 6 copies · chains A, B
- BU1 · 1,4-butanediol · additive · 4 copies · chains A, B
- POL · N-propanol · additive · 2 copies · chains A, B
- PDO · 1,3-propandiol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
- HEZ · Hexane-1,6-diol · additive · chains A
- 1BO · 1-butanol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 263 | 0.66 | 0.82 | 46 | HEZ |
| 2 | 338 | 0.66 | 0.80 | 40 | PGR, BU1 |
| 3 | 326 | 0.66 | 0.81 | 36 | BU1 |
| 4 | 279 | 0.65 | 0.81 | 49 | PGR, POL |
| 5 | 323 | 0.60 | 0.77 | 34 | GOL |
Interfaces
1 interface between chains.
- A–B · 1458 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5MED · Cyanothece lipoxygenase 2 (CspLOX2) · the same entry in another collection · chain A 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 B7JX99
- Elsewhere: RCSB PDB 5MED · PDBe 5MED · UniProt B7JX99
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