MolNFT v1 · #71454 · protein
Crystal structure of choline kinase from cryptosporidium parvum iowa II, CGD3_2030
3MES: “Crystal structure of choline kinase from cryptosporidium parvum iowa II, CGD3_2030”. X-ray diffraction, 4 ligands (ADP, DME, PT3), 8 pockets (best druggability 0.80). MolNFT v1 #71454 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3MES
- Type
- protein
- Length
- 715 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Choline kinase
- UniProt
- Q5CUP2
- Ligands
- ADP, DME, PT3, MG
- Pockets
- 8 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Choline kinase | protein | 357 | 50% helix, 14% strand | Q5CUP2 |
| B | Choline kinase | protein | 358 | 49% helix, 14% strand | Q5CUP2 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- DME · Decamethonium ion · ligand · 2 copies · chains A, B
- PT3 · N-propyl-tartramic acid · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.80 | 0.81 | 73 | ADP, MG, DME, PT3, GOL |
| 2 | 1114 | 0.80 | 0.81 | 85 | ADP, MG, DME, PT3 |
| 3 | 51 | 0.72 | 0.99 | 15 | empty |
| 4 | 52 | 0.72 | 0.99 | 15 | empty |
| 5 | 649 | 0.65 | 0.75 | 38 | empty |
Interfaces
1 interface between chains.
- A–B · 1357 Ų buried · 17 hydrogen bonds · protein-protein
Compared structures
- 3MES · Crystal structure of choline kinase from Cryptosporidium parvum Iowa II, cgd3_2030 · 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 Q5CUP2
- Elsewhere: RCSB PDB 3MES · PDBe 3MES · UniProt Q5CUP2
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