MolNFT v1 · #80783 · protein
Crystal structure of mpnkp catalytic fragment (D170A)
3U7E · Bifunctional polynucleotide PHOSPHATASE/KINASE: “Crystal structure of mpnkp catalytic fragment (D170A)”. X-ray diffraction, 2 ligands (MG, PO4), 5 pockets (best druggability 0.67). MolNFT v1 #80783 on GenesisL1: 3D structure…
- PDB
- 3U7E
- 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, PO4
- Pockets
- 5 · best druggability 0.67
Structure
x-ray diffraction · 1 distinct chain · 35% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 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 B
- PO4 · Phosphate ion · ion · chains B
- GOL · Glycerol · additive · 5 copies · chains B
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 | 646 | 0.67 | 0.76 | 67 | PO4, MG |
| 2 | 178 | 0.59 | 0.82 | 27 | empty |
| 3 | 104 | 0.46 | 0.79 | 22 | GOL |
| 4 | 70 | 0.31 | 0.75 | 17 | GOL |
| 5 | 50 | 0.25 | 0.73 | 14 | empty |
Modifications
Observed in the structure: 6 modified (engineered, oxidation).
Compared structures
- 3U7E · Crystal structure of mPNKP catalytic fragment (D170A) · the same entry in another collection · chain B against B, 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 3U7E · PDBe 3U7E · UniProt Q9JLV6
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