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Crystal structure of archaeoglobus fulgidus argonaute protein with cognate DNA oligoduplex 5'-pattgtggccacaat
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
- 6T5T
- Type
- protein + DNA
- Length
- 432 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*GP*GP*CP*CP*AP*CP*AP*AP*TP)-3'
- UniProt
- O28951
- Ligands
- MG, K, CL
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Piwi protein AF_1318 | protein | 404 | 37% helix, 24% strand | O28951 |
| R, S | 5'-D(*AP*TP*TP*GP*TP*GP*GP*CP*CP*AP*CP*AP*AP*TP)-3' | dna | 14 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, R
- K · Potassium ion · metal · 3 copies · chains A
- CL · Chloride ion · ion · chains A
- BME · Beta-mercaptoethanol · additive · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.58 | 0.80 | 33 | empty |
| 2 | 234 | 0.47 | 0.74 | 22 | empty |
| 3 | 118 | 0.46 | 0.79 | 24 | BME |
| 4 | 76 | 0.39 | 0.78 | 20 | BME |
| 5 | 107 | 0.38 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- A–R · 710 Ų buried · 25 hydrogen bonds · protein-nucleic
- R–S · 582 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- A–S · 380 Ų buried · 7 hydrogen bonds · protein-nucleic
Compared structures
- 6T5T · 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 6T5T · PDBe 6T5T · UniProt O28951
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