Research workbench
Structure of T4PNKP 3' phosphatase covalently bound to BEF3
Analyse Structure of T4PNKP 3' phosphatase covalently bound to BEF3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5UJ0
- Type
- protein
- Length
- 285 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polynucleotide kinase
- EC
- 2.7.1.78, 3.1.3.34
- UniProt
- P06855
- Ligands
- MG
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polynucleotide kinase (EC 2.7.1.78, 3.1.3.34) | protein | 143 | 38% helix, 22% strand | P06855 |
| B | Polynucleotide kinase (EC 2.7.1.78, 3.1.3.34) | protein | 142 | 36% helix, 23% strand | P06855 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.43 | 0.77 | 24 | empty |
| 2 | 92 | 0.36 | 0.76 | 23 | empty |
| 3 | 53 | 0.25 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 837 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nonstandard).
Compared structures
- 5UJ0 · Structure of T4Pnkp 3' phosphatase covalently bound to BeF3 · 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 P06855
- Elsewhere: RCSB PDB 5UJ0 · PDBe 5UJ0 · UniProt P06855
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