Research workbench
Structure of biosynthetic N-acetylornithine aminotransferase from salmonella typhimurium: studies on substrate specificity and inhibitor binding
Analyse Structure of biosynthetic N-acetylornithine aminotransferase from salmonella… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PB0
- Type
- protein
- Length
- 776 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- ACETYLORNITHINE/SUCCINYLDIAMINOPIMELATE aminotransferase
- EC
- 2.6.1.11, 2.6.1.17
- UniProt
- P40732
- Ligands
- PLP
- Pockets
- 3 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | ACETYLORNITHINE/SUCCINYLDIAMINOPIMELATE aminotransferase (EC 2.6.1.11, 2.6.1.17) | protein | 389 | 43% helix, 20% strand | P40732 |
| B | ACETYLORNITHINE/SUCCINYLDIAMINOPIMELATE aminotransferase (EC 2.6.1.11, 2.6.1.17) | protein | 387 | 42% helix, 19% strand | P40732 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1110 | 0.83 | 0.84 | 115 | PLP, EDO |
| 2 | 443 | 0.71 | 0.81 | 47 | empty |
| 3 | 62 | 0.71 | 0.97 | 25 | PLP |
Interfaces
1 interface between chains.
- A–B · 3755 Ų buried · 38 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 2PB0 · Structure of biosynthetic N-acetylornithine aminotransferase from Salmonella typhimurium… · the same entry in another collection · chain A against A, TM-score 1.00
- P40732 · AlphaFold monomer V2.0 prediction for ACETYLORNITHINE/SUCCINYLDIAMINOPIMELATE… · a predicted model of the same protein · chain B 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 P40732
- Elsewhere: RCSB PDB 2PB0 · PDBe 2PB0 · UniProt P40732
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