MolNFT v1 · #17328 · protein
The crystal structure of the complex between stearoyl acyl carrier protein desaturase from ricinus communis (castor bean) and azide.
1OQ4 · Acyl-[acyl-carrier protein] desaturase: “The crystal structure of the complex between stearoyl acyl carrier protein desaturase from ricinus communis…”. X-ray diffraction, 2 ligands (FE, AZI), 20 pockets (best druggability 0.83).…
- PDB
- 1OQ4
- Type
- protein
- Length
- 2,076 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Acyl-[acyl-carrier protein] desaturase
- EC
- 1.14.19.2
- UniProt
- P22337
- Ligands
- FE, AZI
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 66% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F | Acyl-[acyl-carrier protein] desaturase (EC 1.14.19.2) | protein | 346 | 66% helix, 2% strand | P22337 |
Ligands and binding sites
- FE · Fe (III) ion · metal · 12 copies · chains A, B, C, D, E, F
- AZI · Azide ion · ion · 6 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.83 | 0.84 | 106 | empty |
| 2 | 1000 | 0.82 | 0.84 | 105 | empty |
| 3 | 475 | 0.77 | 0.85 | 58 | AZI |
| 4 | 490 | 0.75 | 0.84 | 65 | AZI |
| 5 | 479 | 0.75 | 0.84 | 62 | AZI |
Interfaces
9 interfaces between chains.
- C–D · 2900 Ų buried · 50 hydrogen bonds · protein-protein
- A–B · 2887 Ų buried · 49 hydrogen bonds · protein-protein
- E–F · 2882 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 703 Ų buried · 2 hydrogen bonds · protein-protein
- D–E · 691 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 1OQ4 · The Crystal Structure of the Complex between Stearoyl Acyl Carrier Protein Desaturase… · the same entry in another collection · chain B against B, TM-score 1.00
- P22337 · AlphaFold monomer V2.0 prediction for stearoyl-[acyl-carrier-protein] 9-desaturase… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P22337
- Elsewhere: RCSB PDB 1OQ4 · PDBe 1OQ4 · UniProt P22337
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