MolNFT v1 · #149532 · protein + DNA + RNA
Avaii restriction endonuclease in complex with an RNA/DNA hybrid
6G3B · Type II site-specific deoxyribonuclease: “Avaii restriction endonuclease in complex with an RNA/DNA hybrid”. X-ray diffraction, 7 pockets (best druggability 0.76). MolNFT v1 #149532 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6G3B
- Type
- protein + DNA + RNA
- Length
- 472 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II site-specific deoxyribonuclease; RNA (5'-R(P*GP*UP*AP*GP*GP*AP*CP*CP*AP*UP*G)-3')…
- UniProt
- Q8YYB7
- Pockets
- 7 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II site-specific deoxyribonuclease | protein | 225 | 52% helix, 11% strand | Q8YYB7 |
| B | Type II site-specific deoxyribonuclease | protein | 225 | 49% helix, 11% strand | Q8YYB7 |
| C | RNA (5'-R(P*GP*UP*AP*GP*GP*AP*CP*CP*AP*UP*G)-3') | rna | 11 | — | — |
| D | DNA (5'-D(*CP*CP*AP*TP*GP*GP*TP*CP*CP*TP*A)-3') | dna | 11 | — | — |
Pockets
7 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1142 | 0.76 | 0.79 | 81 | empty |
| 2 | 476 | 0.69 | 0.80 | 45 | empty |
| 3 | 58 | 0.69 | 0.96 | 22 | empty |
| 4 | 55 | 0.68 | 0.97 | 18 | empty |
| 5 | 54 | 0.68 | 0.96 | 22 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2326 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 502 Ų buried · 44 hydrogen bonds · nucleic-nucleic
- A–C · 383 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–D · 369 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–D · 228 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 6G3B · AvaII restriction endonuclease in complex with an RNA/DNA hybrid · 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 6G3B · PDBe 6G3B · UniProt Q8YYB7
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