MolNFT v1 · #13964 · protein
Crystal structure of phosphoglycerate kinase from plasmodium falciparum, in the open conformation
1LTK: “Crystal structure of phosphoglycerate kinase from plasmodium falciparum, in the open conformation”. X-ray diffraction, 2 ligands (AMP, SO4), 11 pockets (best druggability 0.82). MolNFT v1 #13964 on GenesisL1: 3D structure, binding…
- PDB
- 1LTK
- 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
- AMP, SO4
- Pockets
- 11 · best druggability 0.82
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 417 | 38% helix, 18% strand | P27362 |
| B | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 415 | 37% helix, 17% strand | P27362 |
| C | Phosphoglycerate kinase (EC 2.7.2.3) | protein | 424 | 39% helix, 18% strand | P27362 |
Ligands and binding sites
- AMP · Adenosine monophosphate · ligand · 3 copies · chains A, B, C
- SO4 · Sulfate ion · ion · 3 copies · chains A, B, C
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 660 | 0.82 | 0.87 | 82 | AMP |
| 2 | 620 | 0.82 | 0.87 | 70 | AMP |
| 3 | 448 | 0.74 | 0.84 | 75 | SO4 |
| 4 | 120 | 0.56 | 0.84 | 29 | empty |
| 5 | 256 | 0.55 | 0.77 | 42 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 1977 Ų buried · 22 hydrogen bonds · protein-protein
- A–C · 172 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 110 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 25 modified (engineered).
Compared structures
- 1LTK · Crystal structure of phosphoglycerate kinase from plasmodium falciparum, in the open… · 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 1LTK · PDBe 1LTK · UniProt P27362
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