MolNFT v1 · #14581 · protein
Crystal structure of arnb transferase with pyridoxal 5' phosphate
1MDX · Arnb aminotransferase: “Crystal structure of arnb transferase with pyridoxal 5' phosphate”. X-ray diffraction, 2 ligands (PLP, AKG), 3 pockets (best druggability 0.53). MolNFT v1 #14581 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1MDX
- Type
- protein
- Length
- 366 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arnb aminotransferase
- UniProt
- Q8ZNF3
- Ligands
- PLP, AKG
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arnb aminotransferase | protein | 366 | 43% helix, 16% strand | Q8ZNF3 |
Ligands and binding sites
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
- AKG · 2-oxoglutaric acid · ligand · chains A
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.53 | 0.83 | 24 | PLP |
| 2 | 73 | 0.30 | 0.73 | 13 | empty |
| 3 | 54 | 0.26 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).
Compared structures
- 1MDX · Crystal structure of ArnB transferase with pyridoxal 5' phosphate · the same entry in another collection · chain A against A, TM-score 1.00
- Q8ZNF3 · AlphaFold monomer V2.0 prediction for udp-4-amino-4-deoxy-L-arabinose --oxoglutarate… · 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 Q8ZNF3
- Elsewhere: RCSB PDB 1MDX · PDBe 1MDX · UniProt Q8ZNF3
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