Research workbench

Human transketolase variant T382E

Analyse Human transketolase variant T382E in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6RJB
Type: protein
Length: 1,242 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Transketolase
EC: 2.2.1.1
UniProt: P29401
Ligands: TPP, MG, CA, NA
Pockets: 18 · best druggability 0.75

Structure

x-ray diffraction · 2 distinct chains · 41% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Transketolase (EC 2.2.1.1)	protein	620	41% helix, 17% strand	P29401
B	Transketolase (EC 2.2.1.1)	protein	622	42% helix, 17% strand	P29401

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A
EDO · 1,2-ethanediol · additive · 40 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B
PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B

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

Pockets

18 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	297	0.75	0.88	47	TPP, GOL
2	287	0.74	0.87	47	EDO, TPP
3	54	0.72	0.99	23	EDO
4	99	0.68	0.92	24	EDO, PEG
5	112	0.66	0.89	29	PEG, EDO

Interfaces

1 interface between chains.

A–B · 3923 Å² buried · 100 hydrogen bonds · protein-protein

Compared structures

6RJB · Human transketolase variant T382E · the same entry in another collection · chain A against A, TM-score 1.00
P29401 · AlphaFold monomer V2.0 prediction for transketolase (P29401) · 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 P29401
Elsewhere: RCSB PDB 6RJB · PDBe 6RJB · UniProt P29401

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