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Thiamin phosphate synthase

Analyse Thiamin phosphate synthase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1G69
Type: protein
Length: 454 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thiamin phosphate synthase
EC: 2.5.1.3
UniProt: P39594
Ligands: ICP, POP, TZP, MG
Pockets: 5 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 43% helix, 15% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thiamin phosphate synthase (EC 2.5.1.3)	protein	226	43% helix, 15% strand	P39594
B	Thiamin phosphate synthase (EC 2.5.1.3)	protein	228	42% helix, 15% strand	P39594

Ligands and binding sites

ICP · 2-methyl-5-methylene-5H-pyrimidin-4-ylideneamine · ligand · 2 copies · chains A, B
POP · Pyrophosphate 2- · ligand · 2 copies · chains A, B
TZP · 4-methyl-5-hydroxyethylthiazole phosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 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, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	305	0.77	0.89	40	MG, ICP, POP, TZP
2	244	0.75	0.89	40	MG, ICP, POP, TZP
3	170	0.63	0.85	28	empty
4	101	0.58	0.86	31	empty
5	59	0.40	0.81	16	empty

Interfaces

1 interface between chains.

A–B · 904 Å² buried · 18 hydrogen bonds · protein-protein

Compared structures

1G69 · Thiamin phosphate synthase · the same entry in another collection · chain A against A, TM-score 1.00
P39594 · AlphaFold monomer V2.0 prediction for thiamine-phosphate synthase (P39594) · a predicted model of the same protein · chain A against A, TM-score 0.98

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 P39594
Elsewhere: RCSB PDB 1G69 · PDBe 1G69 · UniProt P39594

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