MolNFT v1 · #159782 · protein
Cryptosporidium parvum pyruvate kinase in complex with ADP
6P0Y: “Cryptosporidium parvum pyruvate kinase in complex with ADP”. X-ray diffraction, 4 ligands (ADP, MG, K), 17 pockets (best druggability 0.85). MolNFT v1 #159782 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6P0Y
- Type
- protein
- Length
- 1,002 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
- ADP, MG, K, CL
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 502 | 37% helix, 22% strand | Q5CSM7 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 500 | 38% helix, 21% strand | Q5CSM7 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- K · Potassium ion · metal · 2 copies · chains A, B
- CL · Chloride ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 916 | 0.85 | 0.86 | 137 | ADP, MG, K |
| 2 | 877 | 0.76 | 0.80 | 47 | empty |
| 3 | 98 | 0.73 | 0.95 | 22 | empty |
| 4 | 417 | 0.65 | 0.78 | 48 | empty |
| 5 | 432 | 0.65 | 0.78 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 2186 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6P0Y · Cryptosporidium parvum pyruvate kinase in complex with ADP · 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 6P0Y · PDBe 6P0Y · UniProt Q5CSM7
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