Research workbench

Crystal structure of TON1374

Analyse Crystal structure of TON1374 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MB0
Type: protein
Length: 1,015 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphopantothenate synthetase
EC: 6.3.2.26
UniProt: B6YXQ1
Pockets: 8 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 54% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Phosphopantothenate synthetase (EC 6.3.2.26)	protein	253	55% helix, 9% strand	B6YXQ1
B	Phosphopantothenate synthetase (EC 6.3.2.26)	protein	257	53% helix, 10% strand	B6YXQ1
D	Phosphopantothenate synthetase (EC 6.3.2.26)	protein	252	54% helix, 11% strand	B6YXQ1

Ligands and binding sites

ACT · Acetate ion · additive · chains D

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

Pockets

8 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	1132	0.84	0.85	106	ACT
2	1110	0.81	0.82	111	empty
3	436	0.80	0.88	59	empty
4	326	0.66	0.81	42	empty
5	85	0.42	0.79	14	empty

Interfaces

5 interfaces between chains.

C–D · 2132 Å² buried · 27 hydrogen bonds · protein-protein
A–B · 2118 Å² buried · 24 hydrogen bonds · protein-protein
A–D · 369 Å² buried · 3 hydrogen bonds · protein-protein
A–C · 225 Å² buried · 1 hydrogen bond · protein-protein
B–C · 93 Å² buried · 0 hydrogen bonds · protein-protein

Compared structures

4MB0 · Crystal structure of TON1374 · the same entry in another collection · chain A against A, TM-score 1.00
B6YXQ1 · AlphaFold monomer V2.0 prediction for 4-phosphopantoate--beta-alanine ligase (B6YXQ1) · 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 B6YXQ1
Elsewhere: RCSB PDB 4MB0 · PDBe 4MB0 · UniProt B6YXQ1

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.