Research workbench
Molecular architecture of mammalian polynucleotide kinase, a DNA repair enzyme
Analyse Molecular architecture of mammalian polynucleotide kinase, a DNA repair enzyme in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1YJ5
- Type
- protein
- Length
- 867 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5' polynucleotide kinase-3' phosphatase catalytic domain; 5' polynucleotide kinase-3'…
- EC
- 2.7.1.78
- UniProt
- Q9JLV6
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 5' polynucleotide kinase-3' phosphatase catalytic domain (EC 2.7.1.78) | protein | 379 | 35% helix, 17% strand | Q9JLV6 |
| B | 5' polynucleotide kinase-3' phosphatase catalytic domain (EC 2.7.1.78) | protein | 383 | 35% helix, 16% strand | Q9JLV6 |
| C | 5' polynucleotide kinase-3' phosphatase fha domain (EC 2.7.1.78) | protein | 105 | 0% helix, 43% strand | Q9JLV6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 12 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1132 | 0.76 | 0.78 | 87 | SO4 |
| 2 | 914 | 0.72 | 0.77 | 73 | empty |
| 3 | 104 | 0.69 | 0.92 | 26 | SO4 |
| 4 | 130 | 0.66 | 0.89 | 21 | SO4 |
| 5 | 486 | 0.62 | 0.75 | 45 | SO4 |
Interfaces
3 interfaces between chains.
- A–B · 692 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 384 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 33 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 modified (engineered).
Compared structures
- 1YJ5 · Molecular architecture of mammalian polynucleotide kinase, a DNA repair enzyme · 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 B 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 1YJ5 · PDBe 1YJ5 · UniProt Q9JLV6
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