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Crystal structure of human thiamin pyrophosphokinase 1

Analyse Crystal structure of human thiamin pyrophosphokinase 1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3S4Y
Type: protein
Length: 448 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thiamin pyrophosphokinase 1
EC: 2.7.6.2
UniProt: Q9H3S4
Ligands: TPP, CA, UNX, SO4
Pockets: 5 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Thiamin pyrophosphokinase 1 (EC 2.7.6.2)	protein	224	26% helix, 35% strand	Q9H3S4

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
UNX · Unknown atom or ion · ion · 9 copies · chains A, B
SO4 · Sulfate ion · ion · 5 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	431	0.73	0.83	62	UNX, TPP, SO4
2	357	0.71	0.84	48	TPP, SO4, UNX
3	196	0.49	0.75	22	UNX
4	164	0.45	0.74	19	empty
5	61	0.38	0.79	11	empty

Interfaces

1 interface between chains.

A–B · 1460 Å² buried · 14 hydrogen bonds · protein-protein

Compared structures

3S4Y · Crystal structure of human thiamin pyrophosphokinase 1 · the same entry in another collection · chain A against A, TM-score 1.00
Q9H3S4 · AlphaFold monomer V2.0 prediction for thiamin pyrophosphokinase 1 (Q9H3S4) · 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 Q9H3S4
Elsewhere: RCSB PDB 3S4Y · PDBe 3S4Y · UniProt Q9H3S4

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