Research workbench

3-phosphoglycerate kinase, mutation R65Q

Analyse 3-phosphoglycerate kinase, mutation R65Q in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1QPG
Type: protein
Length: 415 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3-phosphoglycerate kinase
EC: 2.7.2.3
UniProt: P00560
Ligands: MAP, 3PG
Pockets: 3 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain · 41% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	3-phosphoglycerate kinase (EC 2.7.2.3)	protein	415	41% helix, 18% strand	P00560

Ligands and binding sites

MAP · Magnesium-5'-adenyly-imido-triphosphate · ligand · chains A
3PG · 3-phosphoglyceric acid · ligand · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	179	0.50	0.77	36	empty
2	145	0.49	0.78	34	MAP
3	58	0.28	0.74	14	empty

Compared structures

1QPG · 3-phosphoglycerate kinase, mutation R65Q · the same entry in another collection · chain A against A, TM-score 1.00
P00560 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase (P00560) · 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 P00560
Elsewhere: RCSB PDB 1QPG · PDBe 1QPG · UniProt P00560

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