Research workbench
D34G mutant of pvuii endonuclease complexed with cognate DNA shows that ASP34 is directly involved in DNA recognition and indirectly involved in catalysis
Analyse D34G mutant of pvuii endonuclease complexed with cognate DNA shows that ASP34… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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