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Structure of pig muscle pgk complexed with ATP

Analyse Structure of pig muscle pgk complexed with ATP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1VJD
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, PO4
Pockets: 3 · best druggability 0.52

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphoglycerate kinase (EC 2.7.2.3)	protein	416	41% helix, 18% strand	Q7SIB7

Ligands and binding sites

ATP · Adenosine-5'-triphosphate · ligand · chains A
PO4 · Phosphate ion · ion · 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, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	98	0.52	0.83	26	ATP
2	205	0.50	0.76	27	empty
3	64	0.31	0.75	14	empty

Compared structures

1VJD · Structure of pig muscle PGK complexed with ATP · 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 1VJD · PDBe 1VJD · UniProt Q7SIB7

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