Research workbench
Avaii restriction endonuclease in the absence of nucleic acids
Analyse Avaii restriction endonuclease in the absence of nucleic acids in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S58
- Type
- protein
- Length
- 904 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II site-specific deoxyribonuclease
- UniProt
- Q8YYB7
- Ligands
- CA, UNX
- Pockets
- 12 · best druggability 0.75
Structure
x-ray diffraction · 4 distinct chains · 52% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II site-specific deoxyribonuclease | protein | 233 | 50% helix, 11% strand | Q8YYB7 |
| B | Type II site-specific deoxyribonuclease | protein | 215 | 54% helix, 12% strand | Q8YYB7 |
| C | Type II site-specific deoxyribonuclease | protein | 233 | 53% helix, 11% strand | Q8YYB7 |
| D | Type II site-specific deoxyribonuclease | protein | 223 | 49% helix, 11% strand | Q8YYB7 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 653 | 0.75 | 0.81 | 81 | CA |
| 2 | 416 | 0.61 | 0.76 | 52 | CA |
| 3 | 148 | 0.60 | 0.84 | 24 | empty |
| 4 | 269 | 0.57 | 0.78 | 42 | empty |
| 5 | 120 | 0.53 | 0.82 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2278 Ų buried · 20 hydrogen bonds · protein-protein
- C–D · 2271 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 594 Ų buried · 12 hydrogen bonds · protein-protein
- A–D · 530 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 476 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 6S58 · AvaII restriction endonuclease in the absence of nucleic acids · the same entry in another collection · chain A against A, 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
- Every structure of UniProt Q8YYB7
- Elsewhere: RCSB PDB 6S58 · PDBe 6S58 · UniProt Q8YYB7
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