MolNFT v1 · #25228 · protein

Structure of pig muscle pgk complexed with mgatp

1VJC · Phosphoglycerate kinase: “Structure of pig muscle pgk complexed with mgatp”. X-ray diffraction, 2 ligands (ATP, MG), 4 pockets (best druggability 0.51). MolNFT v1 #25228 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1VJC
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: Q7SIB7
Ligands: ATP, MG
Pockets: 4 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 42% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphoglycerate kinase (EC 2.7.2.3)	protein	416	42% helix, 18% strand	Q7SIB7

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A
MG · Magnesium ion · metal

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

Pockets

4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	205	0.51	0.77	28	empty
2	135	0.50	0.79	37	ATP
3	64	0.31	0.75	15	empty
4	50	0.26	0.75	13	empty

Compared structures

1VJC · Structure of pig muscle PGK complexed with MgATP · the same entry in another collection · chain A against A, TM-score 1.00
Q7SIB7 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase 1 (Q7SIB7) · 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 Q7SIB7
Elsewhere: RCSB PDB 1VJC · PDBe 1VJC · UniProt Q7SIB7

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