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Crystal structure of archaeoglobus fulgidus argonaute protein with cognate DNA oligoduplex 5'-pattgtacgtacaat
Analyse Crystal structure of archaeoglobus fulgidus argonaute protein with cognate DNA… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TUO
- Type
- protein + DNA
- Length
- 433 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Piwi protein AF_1318; 5'-D(*AP*TP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*AP*TP)-3'
- UniProt
- O28951
- Ligands
- MG, CL
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Piwi protein AF_1318 | protein | 405 | 38% helix, 25% strand | O28951 |
| R, S | 5'-D(*AP*TP*TP*GP*TP*AP*CP*GP*TP*AP*CP*AP*AP*TP)-3' | dna | 14 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, R
- CL · Chloride ion · ion · chains A
- GOL · Glycerol · additive · 4 copies · chains A
- BME · Beta-mercaptoethanol · additive · 3 copies · chains A
- PEG · Di(hydroxyethyl)ether · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 221 | 0.59 | 0.81 | 26 | empty |
| 2 | 117 | 0.51 | 0.81 | 26 | empty |
| 3 | 269 | 0.48 | 0.73 | 25 | empty |
Interfaces
3 interfaces between chains.
- A–R · 822 Ų buried · 29 hydrogen bonds · protein-nucleic
- R–S · 596 Ų buried · 58 hydrogen bonds · nucleic-nucleic
- A–S · 433 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 6TUO · Crystal structure of Archaeoglobus fulgidus Argonaute protein with cognate DNA… · the same entry in another collection · chain A against A, TM-score 1.00
- O28951 · AlphaFold monomer V2.0 prediction for piwi protein AF_1318 (O28951) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O28951
- Elsewhere: RCSB PDB 6TUO · PDBe 6TUO · UniProt O28951
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