MolNFT v1 · #126821 · protein
Cyanothece lipoxygenase 2 (CSPLOX2) variant - L304V
5MEE · Arachidonate 15-lipoxygenase: “Cyanothece lipoxygenase 2 (CSPLOX2) variant - L304V”. X-ray diffraction, 1 ligand (FE), 16 pockets (best druggability 0.73). MolNFT v1 #126821 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5MEE
- 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 0.73
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 | 52% helix, 9% strand | B7JX99 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 2 copies · chains A, B
- IMD · Imidazole · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 4 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, 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 | 317 | 0.73 | 0.85 | 54 | GOL, IMD |
| 2 | 328 | 0.73 | 0.85 | 56 | IMD |
| 3 | 299 | 0.65 | 0.81 | 31 | IMD |
| 4 | 293 | 0.64 | 0.80 | 33 | empty |
| 5 | 296 | 0.59 | 0.78 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 1452 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 5MEE · Cyanothece lipoxygenase 2 (CspLOX2) variant - L304V · 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 5MEE · PDBe 5MEE · UniProt B7JX99
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