MolNFT v1 · #74522 · protein
Crystal structure of 3-phosphopglycerate kinase of plasmodium falciparum
3OZ7 · Phosphoglycerate kinase: “Crystal structure of 3-phosphopglycerate kinase of plasmodium falciparum”. X-ray diffraction, 1 ligand (SO4), 4 pockets (best druggability 0.84). MolNFT v1 #74522 on GenesisL1: 3D structure, binding sites…
- PDB
- 3OZ7
- Type
- protein
- Length
- 833 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphoglycerate kinase
- EC
- 2.7.2.3
- UniProt
- P27362
- Ligands
- SO4
- Pockets
- 4 · best druggability 0.84
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 416 | 39% helix, 19% strand | P27362 |
| B | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 417 | 41% helix, 19% strand | P27362 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1090 | 0.84 | 0.85 | 127 | SO4 |
| 2 | 578 | 0.81 | 0.87 | 78 | SO4 |
| 3 | 421 | 0.64 | 0.78 | 41 | empty |
| 4 | 103 | 0.51 | 0.82 | 29 | empty |
Interfaces
1 interface between chains.
- A–B · 2201 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3OZ7 · Crystal Structure of 3-Phosphopglycerate Kinase of Plasmodium falciparum · the same entry in another collection · chain A against A, TM-score 1.00
- P27362 · AlphaFold monomer V2.0 prediction for phosphoglycerate kinase (P27362) · 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 P27362
- Elsewhere: RCSB PDB 3OZ7 · PDBe 3OZ7 · UniProt P27362
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