Research workbench

Plasmoodium vivax phosphoglycerate kinase bound to nitrofuran inhibitor from pegsmear at pH 6.5

Analyse Plasmoodium vivax phosphoglycerate kinase bound to nitrofuran inhibitor from… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YJF
Type: protein
Length: 416 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoglycerate kinase
EC: 2.7.2.3
UniProt: A0A1G4HAR7
Ligands: OTQ
Pockets: 3 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphoglycerate kinase (EC 2.7.2.3)	protein	416	40% helix, 19% strand	A0A1G4HAR7

Ligands and binding sites

OTQ · (2~{S})-2-(5-nitrofuran-2-yl)-2,3,5,6,7,8-hexahydro-1~{H}-[1]benzothiolo[2,3-d]pyrimidin-4-one · ligand · chains A
GOL · Glycerol · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	186	0.50	0.77	23	empty
2	171	0.49	0.77	34	OTQ
3	71	0.32	0.75	16	empty

Compared structures

6YJF · Plasmoodium vivax phosphoglycerate kinase bound to nitrofuran inhibitor from PEGSmear at… · the same entry in another collection · 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 A0A1G4HAR7
Elsewhere: RCSB PDB 6YJF · PDBe 6YJF · UniProt A0A1G4HAR7

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