Research workbench
The structural basis for substrate recognition by mammalian polynucleotide kinase 3' phosphatase
Analyse The structural basis for substrate recognition by mammalian polynucleotide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3ZVL
- Type
- protein
- Length
- 380 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional polynucleotide PHOSPHATASE/KINASE
- EC
- 3.1.3.32, 2.7.1.78
- UniProt
- Q9JLV6
- Ligands
- MG, CL
- Pockets
- 5 · best druggability 0.65
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional polynucleotide PHOSPHATASE/KINASE (EC 3.1.3.32, 2.7.1.78) | protein | 380 | 35% helix, 16% strand | Q9JLV6 |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains A
- GOL · Glycerol · additive · 6 copies · chains A
- ACT · Acetate ion · additive · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.65 | 0.76 | 59 | MG, CL, ACT, GOL |
| 2 | 187 | 0.63 | 0.84 | 27 | ACT |
| 3 | 111 | 0.42 | 0.77 | 23 | GOL |
| 4 | 70 | 0.30 | 0.74 | 17 | ACT |
| 5 | 79 | 0.30 | 0.73 | 21 | empty |
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 3ZVL · The structural basis for substrate recognition by mammalian polynucleotide kinase 3'… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9JLV6 · AlphaFold monomer V2.0 prediction for bifunctional polynucleotide PHOSPHATASE/KINASE… · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9JLV6
- Elsewhere: RCSB PDB 3ZVL · PDBe 3ZVL · UniProt Q9JLV6
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