Research workbench

E.COLI transketolase apoenzyme

Analyse E.COLI transketolase apoenzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RJC
Type: protein
Length: 1,332 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transketolase 1
EC: 2.2.1.1
UniProt: P27302
Ligands: CA, NA
Pockets: 15 · best druggability 0.77

Structure

x-ray diffraction · 2 distinct chains · 48% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transketolase 1 (EC 2.2.1.1)	protein	665	48% helix, 14% strand	P27302
B	Transketolase 1 (EC 2.2.1.1)	protein	667	48% helix, 14% strand	P27302

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 44 copies · chains A, B
GOL · Glycerol · additive · 3 copies · chains A

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

Pockets

15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	378	0.77	0.86	50	CA, EDO
2	357	0.77	0.87	51	EDO, CA
3	315	0.56	0.76	37	EDO
4	302	0.55	0.76	42	EDO, GOL
5	300	0.55	0.76	34	EDO

Interfaces

1 interface between chains.

A–B · 4232 Å² buried · 79 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 1 covalent (additive adduct).

Compared structures

6RJC · E.coli transketolase apoenzyme · the same entry in another collection · chain A against A, TM-score 1.00
P27302 · AlphaFold monomer V2.0 prediction for transketolase 1 (P27302) · 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 P27302
Elsewhere: RCSB PDB 6RJC · PDBe 6RJC · UniProt P27302

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