MolNFT v1 · #63349 · protein + DNA + RNA
Alignment of guide-target seed duplex within an argonaute silencing complex
3F73: “Alignment of guide-target seed duplex within an argonaute silencing complex”. X-ray diffraction, 2 ligands (MG, PO4), 20 pockets (best druggability 0.76). MolNFT v1 #63349 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 3F73
- Type
- protein + DNA + RNA
- Length
- 1,397 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argonaute; DNA (5'- D(P*DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*D…
- UniProt
- Q746M7
- Ligands
- MG, PO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 6 distinct chains · 28% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute | protein | 678 | 28% helix, 28% strand | Q746M7 |
| B | Argonaute | protein | 670 | 27% helix, 29% strand | Q746M7 |
| C | DNA (5'- D(P*DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*D A*DTP*DAP*DGP*DT)-3') | dna | 14 | — | — |
| H | RNA (5'- R(*UP*AP*UP*AP*CP*AP*A*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3') | rna | 11 | — | — |
| X | DNA (5'- D(P*DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*DGP*DTP*D A*DTP*DAP*DGP*DT)-3') | dna | 14 | — | — |
| Y | RNA (5'- R(*UP*AP*UP*AP*CP*AP*A*CP*UP*CP*AP*CP*UP*AP*CP*CP*UP*CP*GP*U)-3') | rna | 10 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1103 | 0.76 | 0.79 | 65 | empty |
| 2 | 857 | 0.74 | 0.79 | 63 | empty |
| 3 | 410 | 0.72 | 0.83 | 49 | empty |
| 4 | 518 | 0.69 | 0.79 | 66 | empty |
| 5 | 207 | 0.60 | 0.81 | 39 | empty |
Interfaces
7 interfaces between chains.
- B–X · 1874 Ų buried · 53 hydrogen bonds · protein-nucleic
- A–C · 1842 Ų buried · 40 hydrogen bonds · protein-nucleic
- A–H · 386 Ų buried · 4 hydrogen bonds · protein-nucleic
- C–H · 381 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- X–Y · 370 Ų buried · 35 hydrogen bonds · nucleic-nucleic
Compared structures
- 3F73 · Alignment of guide-target seed duplex within an argonaute silencing complex · 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 Q746M7
- Elsewhere: RCSB PDB 3F73 · PDBe 3F73 · UniProt Q746M7
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