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Ancestral protein ancthen of phosphomethylpyrimidine kinases family

Analyse Ancestral protein ancthen of phosphomethylpyrimidine kinases family in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7R8Y
Type: protein
Length: 438 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphomethylpyrimidine kinase
EC: 2.7.4.7
Ligands: HMH
Pockets: 3 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains · 44% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphomethylpyrimidine kinase (EC 2.7.4.7)	protein	228	45% helix, 24% strand	—
B	Phosphomethylpyrimidine kinase (EC 2.7.4.7)	protein	210	43% helix, 19% strand	—

Ligands and binding sites

HMH · 4-amino-5-hydroxymethyl-2-methylpyrimidine · 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, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	163	0.51	0.79	35	empty
2	168	0.51	0.78	31	HMH
3	88	0.50	0.83	22	empty

Interfaces

1 interface between chains.

A–B · 1052 Å² buried · 10 hydrogen bonds · protein-protein

Compared structures

7R8Y · Ancestral protein AncThEn of Phosphomethylpyrimidine kinases family · 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
Elsewhere: RCSB PDB 7R8Y · PDBe 7R8Y

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