MolNFT v1 · #14583 · protein
Crystal structure of arnb aminotransferase with cycloserine and pyridoxal 5' phosphate
1MDZ: “Crystal structure of arnb aminotransferase with cycloserine and pyridoxal 5' phosphate”. X-ray diffraction, 2 ligands (DCS, PLP), 2 pockets (best druggability 0.49). MolNFT v1 #14583 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1MDZ
- Type
- protein
- Length
- 364 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Arnb aminotransferase
- UniProt
- Q8ZNF3
- Ligands
- DCS, PLP
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 1 distinct chain · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Arnb aminotransferase | protein | 364 | 43% helix, 17% strand | Q8ZNF3 |
Ligands and binding sites
- DCS · D-[3-hydroxy-2-methyl-5-phosphonooxymethyl-pyridin-4-ylmethyl]-N,O-cycloserylamide · ligand · chains A
- PLP · Pyridoxal-5'-phosphate · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.49 | 0.81 | 25 | DCS, PLP |
| 2 | 53 | 0.26 | 0.73 | 15 | empty |
Modifications
Observed in the structure: 1 cofactor, 1 covalent (pyridoxal phosphate Schiff base, covalent ligand).
Compared structures
- 1MDZ · Crystal structure of ArnB aminotransferase with cycloserine and 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 1MDZ · PDBe 1MDZ · UniProt Q8ZNF3
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