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Crystal structure of 7-keto-8-aminopelargonic acid bound 7,8- diaminopelargonic acid synthase in bacillus subtilis
Analyse Crystal structure of 7-keto-8-aminopelargonic acid bound 7,8- diaminopelargonic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DU4
- Type
- protein
- Length
- 896 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
- EC
- 2.6.1.62
- UniProt
- P53555
- Ligands
- PLP, KAP
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 448 | 42% helix, 18% strand | P53555 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- KAP · 7-keto-8-aminopelargonic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 634 | 0.81 | 0.86 | 77 | PLP, KAP |
| 2 | 593 | 0.80 | 0.85 | 72 | PLP, KAP |
| 3 | 98 | 0.36 | 0.74 | 19 | empty |
| 4 | 65 | 0.35 | 0.77 | 13 | empty |
| 5 | 91 | 0.33 | 0.73 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 5586 Ų buried · 67 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor, 2 modified (pyridoxal phosphate Schiff base, oxidation).
Compared structures
- 3DU4 · Crystal structure of 7-keto-8-aminopelargonic acid bound 7,8-diaminopelargonic acid… · the same entry in another collection · chain B against B, TM-score 1.00
- P53555 · AlphaFold monomer V2.0 prediction for L-lysine-- 8-amino-7-oxononanoate transaminase… · a predicted model of the same protein · chain A 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 P53555
- Elsewhere: RCSB PDB 3DU4 · PDBe 3DU4 · UniProt P53555
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