MolNFT v1 · #23047 · protein

Crystal structure of thi-4 protein from bacillus subtilis

1TO9: “Crystal structure of thi-4 protein from bacillus subtilis”. X-ray diffraction, 1 ligand (HMH), 8 pockets (best druggability 0.76). MolNFT v1 #23047 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1TO9
Type: protein
Length: 448 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Thi-4 protein
UniProt: P25052
Ligands: HMH
Pockets: 8 · best druggability 0.76

Structure

x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Thi-4 protein	protein	225	78% helix, 0% strand	P25052
B	Thi-4 protein	protein	223	75% helix, 0% strand	P25052

Ligands and binding sites

HMH · 4-amino-5-hydroxymethyl-2-methylpyrimidine · ligand · 2 copies · chains A, B

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

Pockets

8 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	231	0.76	0.90	37	HMH
2	161	0.68	0.87	25	HMH
3	356	0.66	0.80	32	empty
4	141	0.44	0.76	17	empty
5	85	0.34	0.74	16	empty

Interfaces

1 interface between chains.

A–B · 1259 Å² buried · 22 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered, oxidation).

Compared structures

1TO9 · Crystal structure of THI-4 protein from Bacillus subtilis · the same entry in another collection · chain A against A, TM-score 1.00
P25052 · AlphaFold monomer V2.0 prediction for aminopyrimidine aminohydrolase (P25052) · a predicted model of the same protein · chain B 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 P25052
Elsewhere: RCSB PDB 1TO9 · PDBe 1TO9 · UniProt P25052

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