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The crystal structure of the complex between stearoyl acyl carrier protein desaturase from ricinus communis (castor bean) and azide.
Analyse The crystal structure of the complex between stearoyl acyl carrier protein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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