MolNFT v1 · #75611 · protein + DNA
D34G mutant of pvuii endonuclease complexed with cognate DNA shows that ASP34 is directly involved in DNA recognition and indirectly involved in catalysis
3PVI · DNA (5'- D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3'): “D34G mutant of pvuii endonuclease complexed with cognate DNA shows that ASP34 is directly involved in DNA…”. X-ray diffraction, 4 pockets (best druggability 0.80). MolNFT v1…
- PDB
- 3PVI
- Type
- protein + DNA
- Length
- 338 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (5'- D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3'); Protein (pvuii endonuclease)
- UniProt
- P23657
- Pockets
- 4 · best druggability 0.80
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | DNA (5'- D(*TP*GP*AP*CP*CP*AP*GP*CP*TP*GP*GP*TP*C)-3') | dna | 13 | — | — |
| A, B | Protein (pvuii endonuclease) | protein | 156 | 40% helix, 22% strand | P23657 |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 686 | 0.80 | 0.85 | 52 | empty |
| 2 | 430 | 0.67 | 0.80 | 63 | empty |
| 3 | 90 | 0.46 | 0.81 | 14 | empty |
| 4 | 84 | 0.44 | 0.81 | 14 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1741 Ų buried · 13 hydrogen bonds · protein-protein
- D–A · 653 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–B · 638 Ų buried · 14 hydrogen bonds · protein-nucleic
- C–D · 593 Ų buried · 35 hydrogen bonds · nucleic-nucleic
- D–B · 488 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 3PVI · D34G mutant of pvuii endonuclease complexed with cognate DNA shows that ASP34 is directly… · the same entry in another collection · chain C against C, TM-score 1.00
- P23657 · AlphaFold monomer V2.0 prediction for type-2 restriction enzyme pvuii (P23657) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P23657
- Elsewhere: RCSB PDB 3PVI · PDBe 3PVI · UniProt P23657
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