Research workbench
Crystal structure of the restriction endonuclease bstyi complex with DNA
Analyse Crystal structure of the restriction endonuclease bstyi complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VRR
- Type
- protein + DNA
- Length
- 434 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)-3'; Bstyi
- EC
- 3.1.21.4
- Pockets
- 6 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | 5'-D(*TP*TP*AP*TP*AP*GP*AP*TP*CP*TP*AP*TP*AP*A)-3' | dna | 14 | — | — |
| A, B | Bstyi (EC 3.1.21.4) | protein | 203 | 41% helix, 25% strand | — |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 633 | 0.73 | 0.80 | 55 | empty |
| 2 | 222 | 0.70 | 0.87 | 36 | empty |
| 3 | 206 | 0.68 | 0.86 | 33 | empty |
| 4 | 94 | 0.45 | 0.80 | 21 | empty |
| 5 | 89 | 0.42 | 0.78 | 15 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1872 Ų buried · 7 hydrogen bonds · protein-protein
- C–B · 815 Ų buried · 18 hydrogen bonds · protein-nucleic
- D–A · 807 Ų buried · 15 hydrogen bonds · protein-nucleic
- C–D · 618 Ų buried · 43 hydrogen bonds · nucleic-nucleic
- D–B · 398 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 1VRR · Crystal structure of the restriction endonuclease BstYI complex with DNA · the same entry in another collection · chain C against C, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 1VRR · PDBe 1VRR
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