MolNFT v1 · #12579 · protein

Crystal structure of threonine synthase from yeast

1KL7: “Crystal structure of threonine synthase from yeast”. X-ray diffraction, 1 ligand (PLP), 5 pockets (best druggability 0.76). MolNFT v1 #12579 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1KL7
Type: protein
Length: 1,018 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Threonine synthase
EC: 4.2.99.2
UniProt: P16120
Ligands: PLP
Pockets: 5 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 45% helix, 13% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Threonine synthase (EC 4.2.99.2)	protein	509	45% helix, 13% strand	P16120

Ligands and binding sites

PLP · Pyridoxal-5'-phosphate · ligand · 2 copies · chains A, B

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

Pockets

5 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	800	0.76	0.80	97	PLP
2	770	0.75	0.79	91	PLP
3	64	0.33	0.76	15	empty
4	72	0.32	0.75	13	empty
5	58	0.32	0.76	16	empty

Interfaces

1 interface between chains.

A–B · 103 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified, 2 cofactor (engineered, pyridoxal phosphate Schiff base).

Compared structures

1KL7 · Crystal Structure of Threonine Synthase from Yeast · the same entry in another collection · chain A against A, TM-score 1.00
P16120 · AlphaFold monomer V2.0 prediction for threonine synthase (P16120) · 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 P16120
Elsewhere: RCSB PDB 1KL7 · PDBe 1KL7 · UniProt P16120

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