MolNFT v1 · #80785 · protein + DNA
Crystal structure of mpnkp catalytic fragment (D170A) bound to single- stranded DNA (tcctap)
3U7G · Bifunctional polynucleotide PHOSPHATASE/KINASE: “Crystal structure of mpnkp catalytic fragment (D170A) bound to single- stranded DNA (tcctap)”. X-ray diffraction, 2 ligands (MG, PO4), 6 pockets (best druggability 0.60). MolNFT v1…
- PDB
- 3U7G
- Type
- protein + DNA
- Length
- 379 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Bifunctional polynucleotide PHOSPHATASE/KINASE; DNA
- EC
- 3.1.3.32, 2.7.1.78
- UniProt
- Q9JLV6
- Ligands
- MG, PO4
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 18% 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 | 34% helix, 18% strand | Q9JLV6 |
| X | DNA | dna | 2 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, X
- PO4 · Phosphate ion · ion · 2 copies · chains A, X
- GOL · Glycerol · additive · 3 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 303 | 0.60 | 0.78 | 38 | empty |
| 2 | 110 | 0.59 | 0.86 | 20 | empty |
| 3 | 189 | 0.50 | 0.77 | 30 | MG |
| 4 | 154 | 0.43 | 0.75 | 25 | PO4 |
| 5 | 83 | 0.40 | 0.78 | 23 | GOL |
Interfaces
1 interface between chains.
- A–X · 522 Ų buried · 12 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 5 modified (engineered).
Compared structures
- 3U7G · Crystal structure of mPNKP catalytic fragment (D170A) bound to single-stranded DNA… · 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 0.96
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 3U7G · PDBe 3U7G · UniProt Q9JLV6
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