Research workbench
Structure of the Y94F mutant of the restriction endonuclease pvuii
Analyse Structure of the Y94F mutant of the restriction endonuclease pvuii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1NI0
- Type
- protein
- Length
- 472 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II restriction enzyme pvuii
- EC
- 3.1.21.4
- UniProt
- P23657
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Type II restriction enzyme pvuii (EC 3.1.21.4) | protein | 157 | 39% helix, 24% strand | P23657 |
| C | Type II restriction enzyme pvuii (EC 3.1.21.4) | protein | 158 | 39% helix, 24% strand | P23657 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.57 | 0.77 | 40 | empty |
| 2 | 235 | 0.49 | 0.75 | 38 | empty |
| 3 | 156 | 0.42 | 0.74 | 29 | empty |
| 4 | 82 | 0.40 | 0.78 | 17 | empty |
| 5 | 88 | 0.39 | 0.77 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1591 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 684 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 39 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 1NI0 · Structure of the Y94F mutant of the restriction endonuclease PvuII · the same entry in another collection · chain A against A, 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 0.94
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 1NI0 · PDBe 1NI0 · UniProt P23657
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