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
- 3ZVN
- Type
- protein + DNA
- Length
- 401 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional polynucleotide PHOSPHATASE/KINASE; 5'-D(*GP*TP*CP*AP*CP)-3'
- EC
- 3.1.3.32, 2.7.1.78
- UniProt
- Q9JLV6
- Ligands
- ADP, MN
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Bifunctional polynucleotide PHOSPHATASE/KINASE (EC 3.1.3.32, 2.7.1.78) | protein | 377 | 36% helix, 15% strand | Q9JLV6 |
| E | 5'-D(*GP*TP*CP*AP*CP)-3' | dna | 4 | — | — |
| F, G, H, I | 5'-D(*GP*TP*CP*AP*CP)-3' | dna | 5 | — | — |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · chains A
- MN · Manganese (II) ion · metal · chains A, E
- GOL · Glycerol · additive · 2 copies · chains A
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 | 345 | 0.67 | 0.81 | 38 | MN, GOL, ADP |
| 2 | 456 | 0.67 | 0.79 | 53 | empty |
| 3 | 325 | 0.63 | 0.79 | 40 | empty |
| 4 | 75 | 0.29 | 0.73 | 14 | empty |
Interfaces
11 interfaces between chains.
- A–G · 736 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–E · 504 Ų buried · 12 hydrogen bonds · protein-nucleic
- A–I · 277 Ų buried · 3 hydrogen bonds · protein-nucleic
- F–H · 226 Ų buried · 27 hydrogen bonds · nucleic-nucleic
- A–H · 161 Ų buried · 4 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 3ZVN · The structural basis for substrate recognition by mammalian polynucleotide kinase 3'… · the same entry in another collection · chain F against F, 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 0.97
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 3ZVN · PDBe 3ZVN · UniProt Q9JLV6
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