MolNFT v1 · #170041 · protein + DNA
Archaeoglobus fulgidus argonaute protein with DNA oligoduplex 5'- patcgtggccacgat
6XUP · Piwi protein: “Archaeoglobus fulgidus argonaute protein with DNA oligoduplex 5'- patcgtggccacgat”. X-ray diffraction, 3 ligands (MG, K, CL), 11 pockets (best druggability 0.62). MolNFT v1 #170041 on GenesisL1: 3D structure, binding…
- PDB
- 6XUP
- Type
- protein + DNA
- Length
- 828 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, CL
- Pockets
- 11 · best druggability 0.62
Structure
x-ray diffraction · 6 distinct chains · 38% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Piwi protein | protein | 402 | 38% helix, 25% strand | A0A101DYI0 |
| R | 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 | 5 | — | — |
| B | Piwi protein | protein | 401 | 38% helix, 26% strand | A0A101DYI0 |
| P | 5'-D(*AP*TP*CP*GP*TP*GP*GP*CP*CP*AP*CP*GP*AP*TP)-3' | dna | 6 | — | — |
| 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 · 3 copies · chains A, R, B, P
- K · Potassium ion · metal · chains A
- CL · Chloride ion · ion · chains A
- BME · Beta-mercaptoethanol · additive · 7 copies · chains A, B
- GOL · Glycerol · additive · 7 copies · chains A, B, P
- CAC · Cacodylate ion · additive · 2 copies · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 229 | 0.62 | 0.81 | 30 | GOL |
| 2 | 222 | 0.61 | 0.81 | 32 | empty |
| 3 | 425 | 0.57 | 0.74 | 30 | GOL |
| 4 | 282 | 0.52 | 0.75 | 24 | empty |
| 5 | 110 | 0.50 | 0.81 | 26 | empty |
Interfaces
7 interfaces between chains.
- A–R · 759 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–B · 757 Ų buried · 8 hydrogen bonds · protein-protein
- B–P · 748 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–Q · 401 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–S · 355 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 6XUP · 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 6XUP · PDBe 6XUP · UniProt A0A101DYI0
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