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Crystal structure analysis of phosphomethylpyrimidine kinase (thid) from thermus thermophilus HB8

Analyse Crystal structure analysis of phosphomethylpyrimidine kinase (thid) from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1UB0
Type: protein
Length: 246 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphomethylpyrimidine kinase
EC: 2.7.4.7
UniProt: Q7SIA0
Ligands: SO4
Pockets: 1 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphomethylpyrimidine kinase (EC 2.7.4.7)	protein	246	42% helix, 24% strand	Q7SIA0

Ligands and binding sites

SO4 · Sulfate ion · ion · chains A
GOL · Glycerol · additive · 4 copies · chains A
DIO · 1,4-diethylene dioxide · additive · 2 copies · 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	434	0.65	0.78	56	GOL

Compared structures

1UB0 · Crystal Structure Analysis of Phosphomethylpyrimidine Kinase (ThiD) from Thermus… · the same entry in another collection · 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 Q7SIA0
Elsewhere: RCSB PDB 1UB0 · PDBe 1UB0 · UniProt Q7SIA0

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