Research workbench
Structure of clostridium thermocellum polynucleotide kinase bound to CTP
Analyse Structure of clostridium thermocellum polynucleotide kinase bound to CTP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4JT2
- Type
- protein
- Length
- 341 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Metallophosphoesterase
- EC
- 2.7.1.78
- UniProt
- A3DJ38
- Ligands
- CTP, MG
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 52% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Metallophosphoesterase (EC 2.7.1.78) | protein | 171 | 51% helix, 22% strand | A3DJ38 |
| B | Metallophosphoesterase (EC 2.7.1.78) | protein | 170 | 52% helix, 21% strand | A3DJ38 |
Ligands and binding sites
- CTP · Cytidine-5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 190 | 0.62 | 0.83 | 20 | empty |
| 2 | 375 | 0.59 | 0.76 | 50 | CTP, MG |
| 3 | 186 | 0.51 | 0.78 | 27 | MG, CTP |
| 4 | 72 | 0.39 | 0.79 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 857 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4JT2 · Structure of Clostridium thermocellum polynucleotide kinase bound to CTP · 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 A3DJ38
- Elsewhere: RCSB PDB 4JT2 · PDBe 4JT2 · UniProt A3DJ38
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.