MolNFT v1 · #76513 · protein
Crystal structures of escherichia COLI aspartate aminotransferase reconstituted with 1-deaza-pyridoxal 5'-phosphate: internal aldimine and stable L-aspartate external aldimine
3QN6: “Crystal structures of escherichia COLI aspartate aminotransferase reconstituted with 1-deaza-pyridoxal…”. X-ray diffraction, 2 ligands (3QN, SO4), 4 pockets (best druggability 0.65). MolNFT v1 #76513 on GenesisL1: 3D structure…
- PDB
- 3QN6
- Type
- protein
- Length
- 395 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aspartate aminotransferase
- EC
- 2.6.1.1
- UniProt
- P00509
- Ligands
- 3QN, SO4
- Pockets
- 4 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aspartate aminotransferase (EC 2.6.1.1) | protein | 395 | 48% helix, 14% strand | P00509 |
Ligands and binding sites
- 3QN · (E)-N~6~-{2-hydroxy-3-methyl-6-[(phosphonooxy) methyl]benzylidene}-L-lysine · ligand · chains A
- SO4 · Sulfate ion · ion · 5 copies · chains A
- EDO · 1,2-ethanediol · additive · 4 copies · chains A
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 | 392 | 0.65 | 0.79 | 64 | 3QN, EDO |
| 2 | 105 | 0.42 | 0.77 | 26 | empty |
| 3 | 69 | 0.39 | 0.79 | 22 | empty |
| 4 | 56 | 0.29 | 0.75 | 15 | EDO |
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 3QN6 · Crystal Structures of Escherichia coli Aspartate Aminotransferase Reconstituted with… · the same entry in another collection · chain A against A, TM-score 1.00
- P00509 · AlphaFold monomer V2.0 prediction for aspartate aminotransferase (P00509) · 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 P00509
- Elsewhere: RCSB PDB 3QN6 · PDBe 3QN6 · UniProt P00509
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