MolNFT v1 · #22702 · protein

Threonine deaminase (biosynthetic) from E. COLI

1TDJ · Biosynthetic threonine deaminase: “Threonine deaminase (biosynthetic) from E. COLI”. X-ray diffraction, 1 ligand (PLP), 3 pockets (best druggability 0.74). MolNFT v1 #22702 on GenesisL1: 3D structure, binding sites and pockets in…

PDB: 1TDJ
Type: protein
Length: 494 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Biosynthetic threonine deaminase
EC: 4.2.1.16
UniProt: P04968
Ligands: PLP
Pockets: 3 · best druggability 0.74

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Biosynthetic threonine deaminase (EC 4.2.1.16)	protein	494	39% helix, 18% strand	P04968

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	721	0.74	0.79	71	PLP
2	135	0.52	0.80	21	empty
3	58	0.30	0.75	18	empty

Modifications

Observed in the structure: 1 cofactor (pyridoxal phosphate Schiff base).

Compared structures

1TDJ · Threonine deaminase (biosynthetic) from E. COLI · the same entry in another collection · chain A against A, TM-score 1.00
P04968 · AlphaFold monomer V2.0 prediction for L-threonine dehydratase biosynthetic ilva (P04968) · a predicted model of the same protein · chain A against A, TM-score 0.92

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 P04968
Elsewhere: RCSB PDB 1TDJ · PDBe 1TDJ · UniProt P04968

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