Research workbench

Split gene transketolase, active alpha2beta2 heterotetramer

Analyse Split gene transketolase, active alpha2beta2 heterotetramer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YAK
Type: protein
Length: 1,186 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.34
Source: Carboxydothermus hydrogenoformans
Molecule: N-terminal component of the split chain transketolase; C-terminal component of the split…
Ligands: MLT, LMR, 8EL, CA, CL
Pockets: 11 · best druggability 0.77

Structure

x-ray diffraction · resolution 1.34 · 2 distinct chains · 47% helix, 16% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
AAA, CCC	N-terminal component of the split chain transketolase	protein	282	50% helix, 11% strand	—
BBB, DDD	C-terminal component of the split chain transketolase	protein	311	45% helix, 20% strand	—

Ligands and binding sites

MLT · D-malate · ligand · 11 copies · chains AAA, BBB, CCC
LMR · (2S)-2-hydroxybutanedioic acid · ligand · 5 copies · chains AAA, DDD
8EL · 2-[3-[(4-azanyl-2-methyl-pyrimidin-5-yl)methyl]-4-methyl-2H-1,3-thiazol-5-yl]ethyl phosphono hydrogen phosphate · ligand · 2 copies · chains AAA, DDD, BBB, CCC
CA · Calcium ion · metal · 4 copies · chains AAA, CCC
CL · Chloride ion · ion · 4 copies · chains AAA, BBB, CCC, DDD

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

Pockets

11 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	334	0.77	0.88	50	8EL
2	345	0.74	0.86	47	8EL, CA
3	167	0.48	0.76	26	empty
4	123	0.45	0.77	17	empty
5	118	0.43	0.76	17	CL

Interfaces

6 interfaces between chains.

BBB–DDD · 2026 Å² buried · 37 hydrogen bonds · protein-protein
AAA–BBB · 1069 Å² buried · 17 hydrogen bonds · protein-protein
CCC–DDD · 1054 Å² buried · 15 hydrogen bonds · protein-protein
AAA–DDD · 1051 Å² buried · 28 hydrogen bonds · protein-protein
BBB–CCC · 1050 Å² buried · 30 hydrogen bonds · protein-protein

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6YAK · PDBe 6YAK

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