MolNFT v1 · #96761 · protein
Structure of clostridium thermocellum polynucleotide kinase bound to datp
4JT4 · Metallophosphoesterase: “Structure of clostridium thermocellum polynucleotide kinase bound to datp”. X-ray diffraction, 3 ligands (DTP, MG, NA), 4 pockets (best druggability 0.62). MolNFT v1 #96761 on GenesisL1: 3D structure…
- PDB
- 4JT4
- Type
- protein
- Length
- 342 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
- DTP, MG, NA
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 1 distinct chain · 50% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Metallophosphoesterase (EC 2.7.1.78) | protein | 171 | 50% helix, 22% strand | A3DJ38 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains 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 | 189 | 0.62 | 0.83 | 19 | empty |
| 2 | 408 | 0.61 | 0.76 | 46 | MG, DTP |
| 3 | 248 | 0.53 | 0.76 | 38 | MG, DTP |
| 4 | 70 | 0.39 | 0.79 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 880 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 modified (engineered).
Compared structures
- 4JT4 · Structure of Clostridium thermocellum polynucleotide kinase bound to dATP · 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 4JT4 · PDBe 4JT4 · UniProt A3DJ38
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