Research workbench
Crystal structure of 7,8 diaminopelargonic acid synthase apoenzyme in bacillus subtilis
Analyse Crystal structure of 7,8 diaminopelargonic acid synthase apoenzyme in bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DRD
- Type
- protein
- Length
- 836 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
- Pockets
- 5 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 44% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 419 | 44% helix, 18% strand | P53555 |
| B | Adenosylmethionine-8-amino-7-oxononanoate aminotransferase (EC 2.6.1.62) | protein | 417 | 43% helix, 19% strand | P53555 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 688 | 0.73 | 0.79 | 77 | empty |
| 2 | 222 | 0.71 | 0.87 | 29 | empty |
| 3 | 190 | 0.68 | 0.86 | 26 | empty |
| 4 | 96 | 0.36 | 0.74 | 15 | empty |
| 5 | 58 | 0.29 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 4406 Ų buried · 57 hydrogen bonds · protein-protein
Compared structures
- 3DRD · Crystal Structure of 7,8 Diaminopelargonic Acid Synthase Apoenzyme in Bacillus subtilis · the same entry in another collection · chain A against A, 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 3DRD · PDBe 3DRD · UniProt P53555
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