MolNFT v1 · #157843 · protein
The structure of stable-5-lipoxygenase bound to akba
6NCF · Arachidonate 5-lipoxygenase: “The structure of stable-5-lipoxygenase bound to akba”. X-ray diffraction, 2 ligands (AF7, FE2), 20 pockets (best druggability 0.84). MolNFT v1 #157843 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6NCF
- Type
- protein
- Length
- 2,689 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arachidonate 5-lipoxygenase
- EC
- 1.13.11.34
- UniProt
- P09917
- Ligands
- AF7, FE2
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 3 distinct chains · 44% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arachidonate 5-lipoxygenase (EC 1.13.11.34) | protein | 675 | 44% helix, 13% strand | P09917 |
| B | Arachidonate 5-lipoxygenase (EC 1.13.11.34) | protein | 676 | 44% helix, 13% strand | P09917 |
| C, D | Arachidonate 5-lipoxygenase (EC 1.13.11.34) | protein | 669 | 44% helix, 13% strand | P09917 |
Ligands and binding sites
- AF7 · (3alpha,8alpha,17alpha,18alpha)-3-(acetyloxy)-11-oxours-12-en-23-oic acid · ligand · chains B
- FE2 · Fe (II) ion · metal · 4 copies · chains A, B, C, D
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 | 1127 | 0.84 | 0.85 | 106 | empty |
| 2 | 1188 | 0.84 | 0.85 | 118 | empty |
| 3 | 111 | 0.80 | 0.98 | 32 | empty |
| 4 | 104 | 0.79 | 0.98 | 25 | empty |
| 5 | 710 | 0.79 | 0.83 | 80 | empty |
Interfaces
4 interfaces between chains.
- A–C · 980 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 880 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 574 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 475 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6NCF · The structure of Stable-5-Lipoxygenase bound to AKBA · 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 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 P09917
- Elsewhere: RCSB PDB 6NCF · PDBe 6NCF · UniProt P09917
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