MolNFT v1 · #54087 · protein

The complete reaction cycle of human phosphoglycerate kinase: the open binary complex with 3PG

2XE6 · Phosphoglycerate kinase 1: “The complete reaction cycle of human phosphoglycerate kinase: the open binary complex with 3PG”. X-ray diffraction, 1 ligand (3PG), 2 pockets (best druggability 0.52). MolNFT v1 #54087 on GenesisL1: 3D…

PDB: 2XE6
Type: protein
Length: 413 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: 3PG
Pockets: 2 · best druggability 0.52

Structure

x-ray diffraction · 1 distinct chain · 40% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Phosphoglycerate kinase 1 (EC 2.7.2.3)	protein	413	40% helix, 18% strand	P00558

Ligands and binding sites

3PG · 3-phosphoglyceric acid · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	228	0.52	0.77	37	3PG
2	142	0.49	0.78	33	empty

Compared structures

2XE6 · The complete reaction cycle of human phosphoglycerate kinase: The open binary complex… · 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 0.97

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 2XE6 · PDBe 2XE6 · UniProt P00558

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