MolNFT v1 · #112163 · protein
Crystal structure of the C-terminal catalytic domain of plasmodium falciparum CTP:PHOSPHOCHOLINE cytidylyltransferase in complex with cdp-choline
4ZCS · Choline-phosphate cytidylyltransferase: “Crystal structure of the C-terminal catalytic domain of plasmodium falciparum CTP:PHOSPHOCHOLINE…”. X-ray diffraction, 1 ligand (CDC), 13 pockets (best druggability 0.68). MolNFT v1 #112163…
- PDB
- 4ZCS
- Type
- protein
- Length
- 839 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Choline-phosphate cytidylyltransferase
- EC
- 2.7.7.15
- UniProt
- Q8IEE9
- Ligands
- CDC
- Pockets
- 13 · best druggability 0.68
Structure
x-ray diffraction · 5 distinct chains · 34% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Choline-phosphate cytidylyltransferase (EC 2.7.7.15) | protein | 141 | 34% helix, 22% strand | Q8IEE9 |
| C | Choline-phosphate cytidylyltransferase (EC 2.7.7.15) | protein | 137 | 33% helix, 23% strand | Q8IEE9 |
| B | Choline-phosphate cytidylyltransferase (EC 2.7.7.15) | protein | 140 | 35% helix, 22% strand | Q8IEE9 |
| D | Choline-phosphate cytidylyltransferase (EC 2.7.7.15) | protein | 139 | 33% helix, 24% strand | Q8IEE9 |
| F | Choline-phosphate cytidylyltransferase (EC 2.7.7.15) | protein | 141 | 35% helix, 23% strand | Q8IEE9 |
Ligands and binding sites
- CDC · [2-cytidylate-O'-phosphonyloxyl]-ethyl-trimethyl-ammonium · ligand · 6 copies · chains A, C, E, B, D, F
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 315 | 0.68 | 0.82 | 35 | CDC |
| 2 | 322 | 0.67 | 0.82 | 40 | CDC |
| 3 | 321 | 0.67 | 0.81 | 38 | CDC |
| 4 | 322 | 0.67 | 0.81 | 40 | CDC |
| 5 | 295 | 0.66 | 0.81 | 37 | CDC |
Interfaces
7 interfaces between chains.
- E–F · 1289 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 1280 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 1168 Ų buried · 20 hydrogen bonds · protein-protein
- A–E · 479 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 413 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 4ZCS · Crystal structure of the C-terminal catalytic domain of Plasmodium falciparum… · 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 Q8IEE9
- Elsewhere: RCSB PDB 4ZCS · PDBe 4ZCS · UniProt Q8IEE9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.