Research workbench
The nuclease domain of adeno-associated virus rep complexed with the rbe' stemloop of the viral inverted terminal repeat
Analyse The nuclease domain of adeno-associated virus rep complexed with the rbe'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1UUT
- Type
- protein + DNA
- Length
- 420 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Rep protein; 5'-D(*CP*AP*GP*CP*TP*CP*TP*TP*TP*GP *AP*GP*CP*TP*G)-3'
- UniProt
- Q9YJC1
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.31
Structure
x-ray diffraction · 2 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Rep protein | protein | 195 | 43% helix, 17% strand | Q9YJC1 |
| C, D | 5'-D(*CP*AP*GP*CP*TP*CP*TP*TP*TP*GP *AP*GP*CP*TP*G)-3' | dna | 15 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.31 | 0.73 | 11 | empty |
| 2 | 58 | 0.29 | 0.74 | 14 | empty |
| 3 | 56 | 0.29 | 0.75 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–B · 438 Ų buried · 3 hydrogen bonds · protein-protein
- B–D · 371 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 366 Ų buried · 11 hydrogen bonds · protein-nucleic
Compared structures
- 1UUT · The Nuclease Domain of Adeno-Associated Virus Rep Complexed with the RBE' Stemloop of the… · 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 Q9YJC1
- Elsewhere: RCSB PDB 1UUT · PDBe 1UUT · UniProt Q9YJC1
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.