MolNFT v1 · #47815 · protein

Crystal structure of phosphoglycerate kinase-2 bound to 3- phosphoglycerate

2P9T · Phosphoglycerate kinase, testis specific: “Crystal structure of phosphoglycerate kinase-2 bound to 3- phosphoglycerate”. X-ray diffraction, 1 ligand (3PG), 3 pockets (best druggability 0.52). MolNFT v1 #47815 on GenesisL1: 3D…

PDB: 2P9T
Type: protein
Length: 413 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Phosphoglycerate kinase, testis specific
EC: 2.7.2.3
UniProt: P09041
Ligands: 3PG
Pockets: 3 · 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, testis specific (EC 2.7.2.3)	protein	413	40% helix, 18% strand	P09041

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

3 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	179	0.52	0.78	31	empty
2	141	0.44	0.77	28	3PG
3	86	0.33	0.74	13	empty

Compared structures

2P9T · Crystal Structure of Phosphoglycerate Kinase-2 bound to 3-phosphoglycerate · the same entry in another collection · chain A against A, TM-score 1.00
P09041 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase 2 (P09041) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P09041
Elsewhere: RCSB PDB 2P9T · PDBe 2P9T · UniProt P09041

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