MolNFT v1 · #19298 · protein

Transketolase from escherichia COLI

1QGD · Protein (transketolase): “Transketolase from escherichia COLI”. X-ray diffraction, 3 ligands (TPP, CA, SO4), 13 pockets (best druggability 0.77). MolNFT v1 #19298 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1QGD
Type: protein
Length: 1,324 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protein (transketolase)
EC: 2.2.1.1
UniProt: P27302
Ligands: TPP, CA, SO4
Pockets: 13 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 47% helix, 14% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Protein (transketolase) (EC 2.2.1.1)	protein	662	47% helix, 14% strand	P27302

Ligands and binding sites

TPP · Thiamine diphosphate · ligand · 2 copies · chains A, B
CA · Calcium ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 2 copies · chains A, B

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

Pockets

13 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	366	0.77	0.87	50	TPP, SO4
2	354	0.76	0.87	50	SO4, CA, TPP
3	806	0.70	0.76	93	empty
4	211	0.50	0.76	29	empty
5	235	0.49	0.75	34	empty

Interfaces

1 interface between chains.

A–B · 4257 Å² buried · 69 hydrogen bonds · protein-protein

Compared structures

1QGD · Transketolase from escherichia COLI · 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 1.00

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 1QGD · PDBe 1QGD · UniProt P27302

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