Research workbench
Archaeoglobus fulgidus argonaute protein with DNA oligoduplex 5'- patcgtggccacgat
Analyse Archaeoglobus fulgidus argonaute protein with DNA oligoduplex 5'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XU0
- Type
- protein + DNA
- Length
- 830 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Piwi protein; 5'-D(*AP*TP*CP*GP*TP*GP*GP*CP*CP*AP*CP*GP*AP*TP)-3'
- UniProt
- A0A101DYI0
- Ligands
- MG, K
- Pockets
- 11 · best druggability 0.62
Structure
x-ray diffraction · 5 distinct chains · 38% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Piwi protein | protein | 402 | 38% helix, 25% strand | A0A101DYI0 |
| R, P | 5'-D(*AP*TP*CP*GP*TP*GP*GP*CP*CP*AP*CP*GP*AP*TP)-3' | dna | 7 | — | — |
| S | 5'-D(*AP*TP*CP*GP*TP*GP*GP*CP*CP*AP*CP*GP*AP*TP)-3' | dna | 6 | — | — |
| B | Piwi protein | protein | 401 | 39% helix, 24% strand | A0A101DYI0 |
| Q | 5'-D(*AP*TP*CP*GP*TP*GP*GP*CP*CP*AP*CP*GP*AP*TP)-3' | dna | 7 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 2 copies · chains A, R, B, P
- K · Potassium ion · metal · chains B
- CAC · Cacodylate ion · additive · 3 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- PG0 · 2-(2-methoxyethoxy)ethanol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 237 | 0.62 | 0.80 | 30 | PG0 |
| 2 | 216 | 0.58 | 0.81 | 29 | empty |
| 3 | 195 | 0.58 | 0.81 | 45 | K |
| 4 | 436 | 0.57 | 0.74 | 28 | empty |
| 5 | 321 | 0.54 | 0.75 | 29 | empty |
Interfaces
7 interfaces between chains.
- A–R · 737 Ų buried · 31 hydrogen bonds · protein-nucleic
- B–P · 715 Ų buried · 23 hydrogen bonds · protein-nucleic
- A–B · 641 Ų buried · 6 hydrogen bonds · protein-protein
- B–Q · 383 Ų buried · 4 hydrogen bonds · protein-nucleic
- A–S · 365 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 6XU0 · Archaeoglobus fulgidus Argonaute protein with DNA oligoduplex 5'-pATCGTGGCCACGAT · 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 A0A101DYI0
- Elsewhere: RCSB PDB 6XU0 · PDBe 6XU0 · UniProt A0A101DYI0
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