MolNFT v1 · #47831 · protein
Crystal structure of phosphoglycerate kinase-2 bound to ATP and 3PG
2PAA · Phosphoglycerate kinase, testis specific: “Crystal structure of phosphoglycerate kinase-2 bound to ATP and 3PG”. X-ray diffraction, 2 ligands (ATP, 3PG), 6 pockets (best druggability 0.58). MolNFT v1 #47831 on GenesisL1: 3D…
- PDB
- 2PAA
- Type
- protein
- Length
- 811 residues
- Chains
- 2
- 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
- ATP, 3PG
- Pockets
- 6 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase, testis specific (EC 2.7.2.3) | protein | 413 | 38% helix, 17% strand | P09041 |
| B | Phosphoglycerate kinase, testis specific (EC 2.7.2.3) | protein | 398 | 38% helix, 18% strand | P09041 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.58 | 0.76 | 49 | empty |
| 2 | 169 | 0.53 | 0.79 | 37 | ATP |
| 3 | 174 | 0.48 | 0.76 | 22 | empty |
| 4 | 59 | 0.38 | 0.79 | 18 | empty |
| 5 | 119 | 0.37 | 0.74 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 353 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 2PAA · Crystal structure of phosphoglycerate kinase-2 bound to atp and 3pg · the same entry in another collection · chain B against B, 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 0.99
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 P09041
- Elsewhere: RCSB PDB 2PAA · PDBe 2PAA · UniProt P09041
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