MolNFT v1 · #14573 · protein

Crystal structure of arnb aminotransferase with pyridomine 5' phosphate

1MDO: “Crystal structure of arnb aminotransferase with pyridomine 5' phosphate”. X-ray diffraction, 1 ligand (PMP), 1 pocket (best druggability 0.54). MolNFT v1 #14573 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1MDO
Type: protein
Length: 365 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Arnb aminotransferase
UniProt: Q8ZNF3
Ligands: PMP
Pockets: 1 · best druggability 0.54

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Arnb aminotransferase	protein	365	42% helix, 16% strand	Q8ZNF3

Ligands and binding sites

PMP · 4'-deoxy-4'-aminopyridoxal-5'-phosphate · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	105	0.54	0.83	24	PMP

Modifications

Observed in the structure: 10 modified (engineered).

Compared structures

1MDO · Crystal structure of ArnB aminotransferase with pyridomine 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 1MDO · PDBe 1MDO · UniProt Q8ZNF3

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