Research workbench
Crystal structure of cryptosporidium parvum pyruvate kinase
Analyse Crystal structure of cryptosporidium parvum pyruvate kinase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DRS
- Type
- protein
- Length
- 970 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pyruvate kinase
- EC
- 2.7.1.40
- UniProt
- Q5CSM7
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.75
Structure
x-ray diffraction · 1 distinct chain · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pyruvate kinase (EC 2.7.1.40) | protein | 485 | 39% helix, 21% strand | Q5CSM7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
- ACT · Acetate ion · additive · 6 copies · chains A, B
- GOL · Glycerol · additive · 4 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, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.75 | 0.79 | 80 | GOL, ACT |
| 2 | 793 | 0.74 | 0.79 | 75 | GOL, ACT |
| 3 | 882 | 0.72 | 0.76 | 54 | empty |
| 4 | 202 | 0.58 | 0.81 | 25 | SO4 |
| 5 | 193 | 0.54 | 0.79 | 25 | SO4 |
Interfaces
1 interface between chains.
- A–B · 2163 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4DRS · Crystal structure of Cryptosporidium parvum pyruvate kinase · the same entry in another collection · chain A against A, TM-score 1.00
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 Q5CSM7
- Elsewhere: RCSB PDB 4DRS · PDBe 4DRS · UniProt Q5CSM7
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