MolNFT v1 · #71300 · protein
Crystal structure of CGD1_2040, a pyruvate kinase from cryptosporidium parvum
3MA8: “Crystal structure of CGD1_2040, a pyruvate kinase from cryptosporidium parvum”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.80). MolNFT v1 #71300 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3MA8
- Type
- protein
- Length
- 985 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
- 12 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pyruvate kinase (EC 2.7.1.40) | protein | 490 | 41% helix, 19% strand | Q5CSM7 |
| B | Pyruvate kinase (EC 2.7.1.40) | protein | 495 | 40% helix, 22% strand | Q5CSM7 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- CIT · Citric acid · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.80 | 0.94 | 37 | empty |
| 2 | 789 | 0.70 | 0.77 | 84 | CIT |
| 3 | 457 | 0.66 | 0.79 | 50 | CIT |
| 4 | 386 | 0.65 | 0.79 | 45 | empty |
| 5 | 275 | 0.63 | 0.81 | 28 | empty |
Interfaces
1 interface between chains.
- A–B · 2245 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3MA8 · Crystal structure of CGD1_2040, a pyruvate kinase from cryptosporidium Parvum · 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 3MA8 · PDBe 3MA8 · UniProt Q5CSM7
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