MolNFT v1 · #11841 · protein
Catalytic mechanism of CTP:PHOSPHOCHOLINE cytidylytransferase from streptococcus pneumoniae (licc)
1JYL: “Catalytic mechanism of CTP:PHOSPHOCHOLINE cytidylytransferase from streptococcus pneumoniae (licc)”. X-ray diffraction, 2 ligands (CDC, MG), 11 pockets (best druggability 0.85). MolNFT v1 #11841 on GenesisL1: 3D structure, binding…
- PDB
- 1JYL
- Type
- protein
- Length
- 912 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- CTP:PHOSPHOCHOLINE cytidylytransferase
- UniProt
- Q97QE9
- Ligands
- CDC, MG
- Pockets
- 11 · best druggability 0.85
Structure
x-ray diffraction · 1 distinct chain · 29% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | CTP:PHOSPHOCHOLINE cytidylytransferase | protein | 228 | 29% helix, 28% strand | Q97QE9 |
Ligands and binding sites
- CDC · [2-cytidylate-O'-phosphonyloxyl]-ethyl-trimethyl-ammonium · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 367 | 0.85 | 0.94 | 46 | MG, CDC |
| 2 | 413 | 0.83 | 0.91 | 54 | MG, CDC |
| 3 | 602 | 0.73 | 0.80 | 58 | MG, CDC |
| 4 | 578 | 0.71 | 0.80 | 55 | MG, CDC |
| 5 | 653 | 0.69 | 0.77 | 70 | empty |
Interfaces
4 interfaces between chains.
- C–D · 746 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 739 Ų buried · 8 hydrogen bonds · protein-protein
- B–C · 504 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 241 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 1JYL · Catalytic Mechanism of CTP:phosphocholine Cytidylyltransferase from Streptococcus… · 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 Q97QE9
- Elsewhere: RCSB PDB 1JYL · PDBe 1JYL · UniProt Q97QE9
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