Research workbench
Avaii restriction endonuclease in complex with partially cleaved dsdna
Analyse Avaii restriction endonuclease in complex with partially cleaved dsdna in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6S48
- Type
- protein + DNA
- Length
- 507 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II site-specific deoxyribonuclease; DNA (5'-D(*GP*AP*TP*GP*GP*TP*CP*CP*TP*AP*C)-3')…
- UniProt
- Q8YYB7
- Ligands
- SER, CA
- Pockets
- 12 · best druggability 0.80
Structure
x-ray diffraction · 7 distinct chains · 56% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II site-specific deoxyribonuclease | protein | 235 | 56% helix, 10% strand | Q8YYB7 |
| B | Type II site-specific deoxyribonuclease | protein | 228 | 57% helix, 11% strand | Q8YYB7 |
| C | DNA (5'-D(*GP*AP*TP*GP*GP*TP*CP*CP*TP*AP*C)-3') | dna | 11 | — | — |
| D, H | DNA (5'-D(*GP*TP*AP*G)-3') | dna | 4 | — | — |
| E, I | DNA (5'-D(P*GP*AP*CP*CP*AP*TP*C)-3') | dna | 7 | — | — |
| F | DNA (5'-D(*GP*AP*TP*G)-3') | dna | 4 | — | — |
| G | DNA (5'-D(P*GP*TP*CP*CP*TP*AP*C)-3') | dna | 7 | — | — |
Ligands and binding sites
- SER · Serine · ligand · chains B
- CA · Calcium ion · metal · 5 copies · chains A, C, I, B, E, G, D, F, H
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · chains B
- PGE · Triethylene glycol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 425 | 0.80 | 0.89 | 49 | CA |
| 2 | 333 | 0.79 | 0.90 | 58 | empty |
| 3 | 56 | 0.67 | 0.96 | 22 | empty |
| 4 | 61 | 0.66 | 0.95 | 24 | empty |
| 5 | 140 | 0.50 | 0.80 | 32 | empty |
Interfaces
34 interfaces between chains.
- A–B · 2400 Ų buried · 22 hydrogen bonds · protein-protein
- C–I · 880 Ų buried · 263 hydrogen bonds · nucleic-nucleic
- E–G · 868 Ų buried · 274 hydrogen bonds · nucleic-nucleic
- A–C · 768 Ų buried · 15 hydrogen bonds · protein-nucleic
- B–C · 630 Ų buried · 8 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 covalent (additive adduct).
Compared structures
- 6S48 · AvaII RESTRICTION ENDONUCLEASE IN COMPLEX WITH PARTIALLY CLEAVED dsDNA · 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 6S48 · PDBe 6S48 · UniProt Q8YYB7
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