Research workbench
Crystal structure of the plp-bound form of 8-amino-7-oxonanoate synthase
Analyse Crystal structure of the plp-bound form of 8-amino-7-oxonanoate synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DJE
- Type
- protein
- Length
- 383 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 8-amino-7-oxonanoate synthase
- EC
- 2.3.1.47
- UniProt
- P12998
- Ligands
- PLP, SO4
- Pockets
- 4 · best druggability 0.64
Structure
x-ray diffraction · 1 distinct chain · 44% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 8-amino-7-oxonanoate synthase (EC 2.3.1.47) | protein | 383 | 44% helix, 18% strand | P12998 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 108 | 0.64 | 0.88 | 20 | empty |
| 2 | 274 | 0.48 | 0.73 | 39 | empty |
| 3 | 70 | 0.32 | 0.75 | 22 | empty |
| 4 | 52 | 0.32 | 0.77 | 11 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1DJE · Crystal structure of the plp-bound form of 8-amino-7-oxonanoate synthase · the same entry in another collection · chain A against A, TM-score 1.00
- P12998 · AlphaFold monomer V2.0 prediction for 8-amino-7-oxononanoate synthase (P12998) · 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 P12998
- Elsewhere: RCSB PDB 1DJE · PDBe 1DJE · UniProt P12998
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