MolNFT v1 · #82000 · protein
S663D stable-5-lox in complex with arachidonic acid
3V99 · Arachidonate 5-lipoxygenase: “S663D stable-5-lox in complex with arachidonic acid”. X-ray diffraction, 2 ligands (ACD, FE2), 12 pockets (best druggability 0.84). MolNFT v1 #82000 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3V99
- Type
- protein
- Length
- 1,269 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arachidonate 5-lipoxygenase
- EC
- 1.13.11.34
- UniProt
- P09917
- Ligands
- ACD, FE2
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arachidonate 5-lipoxygenase (EC 1.13.11.34) | protein | 630 | 46% helix, 14% strand | P09917 |
| B | Arachidonate 5-lipoxygenase (EC 1.13.11.34) | protein | 639 | 44% helix, 15% strand | P09917 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1171 | 0.84 | 0.85 | 118 | empty |
| 2 | 1190 | 0.79 | 0.80 | 115 | empty |
| 3 | 952 | 0.74 | 0.77 | 73 | FE2, ACD |
| 4 | 292 | 0.68 | 0.83 | 40 | empty |
| 5 | 337 | 0.59 | 0.77 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 1153 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 3V99 · S663D Stable-5-LOX in complex with Arachidonic Acid · the same entry in another collection · chain A against A, TM-score 1.00
- P09917 · AlphaFold monomer V2.0 prediction for polyunsaturated fatty acid 5-lipoxygenase (P09917) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 P09917
- Elsewhere: RCSB PDB 3V99 · PDBe 3V99 · UniProt P09917
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