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The crystal structure of the one-iron form of the di-iron center in stearoyl acyl carrier protein desaturase from ricinus communis (castor bean).
Analyse The crystal structure of the one-iron form of the di-iron center in stearoyl… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1OQB
- 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
- FE2
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 65% 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 | 65% helix, 2% strand | P22337 |
Ligands and binding sites
- FE2 · Fe (II) ion · metal · 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, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1060 | 0.83 | 0.84 | 85 | empty |
| 2 | 1148 | 0.82 | 0.83 | 83 | empty |
| 3 | 464 | 0.71 | 0.81 | 54 | empty |
| 4 | 478 | 0.71 | 0.81 | 57 | empty |
| 5 | 468 | 0.70 | 0.81 | 60 | empty |
Interfaces
9 interfaces between chains.
- C–D · 2894 Ų buried · 58 hydrogen bonds · protein-protein
- A–B · 2877 Ų buried · 58 hydrogen bonds · protein-protein
- E–F · 2870 Ų buried · 50 hydrogen bonds · protein-protein
- B–C · 500 Ų buried · 8 hydrogen bonds · protein-protein
- D–E · 500 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 1OQB · The Crystal Structure of the one-iron form of the di-iron center in Stearoyl Acyl Carrier… · the same entry in another collection · chain C against C, 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 1OQB · PDBe 1OQB · UniProt P22337
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