MolNFT v1 · #74524 · protein
Crystal structure of plasmodium falciparum 3-phosphoglycerate kinase
3OZA: “Crystal structure of plasmodium falciparum 3-phosphoglycerate kinase”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.81). MolNFT v1 #74524 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3OZA
- Type
- protein
- Length
- 1,256 residues
- Chains
- 3
- 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
- 14 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 417 | 37% helix, 20% strand | P27362 |
| B | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 415 | 37% helix, 19% strand | P27362 |
| C | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 424 | 40% helix, 18% strand | P27362 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 616 | 0.81 | 0.86 | 73 | SO4 |
| 2 | 657 | 0.81 | 0.86 | 85 | SO4 |
| 3 | 232 | 0.67 | 0.84 | 52 | SO4, GOL |
| 4 | 54 | 0.62 | 0.93 | 27 | empty |
| 5 | 127 | 0.58 | 0.84 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2260 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 190 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 113 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 25 modified (engineered).
Compared structures
- 3OZA · Crystal Structure of Plasmodium falciparum 3-Phosphoglycerate Kinase · 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 B 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 3OZA · PDBe 3OZA · UniProt P27362
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