MolNFT v1 · #129000 · protein

The X-ray structure of human R38M phosphoglycerate kinase 1 mutant

5O7D: “The X-ray structure of human R38M phosphoglycerate kinase 1 mutant”. X-ray diffraction, 1 ligand (ADP), 2 pockets (best druggability 0.55). MolNFT v1 #129000 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5O7D
Type: protein
Length: 415 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoglycerate kinase 1
EC: 2.7.2.3
UniProt: P00558
Ligands: ADP
Pockets: 2 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 39% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphoglycerate kinase 1 (EC 2.7.2.3)	protein	415	39% helix, 19% strand	P00558

Ligands and binding sites

ADP · Adenosine-5'-diphosphate · ligand · chains A

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

Pockets

2 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	306	0.55	0.75	38	empty
2	159	0.53	0.80	37	ADP

Compared structures

5O7D · The X-ray structure of human R38M phosphoglycerate kinase 1 mutant · the same entry in another collection · chain A against A, TM-score 1.00
P00558 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase 1 (P00558) · 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 P00558
Elsewhere: RCSB PDB 5O7D · PDBe 5O7D · UniProt P00558

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