MolNFT v1 · #61436 · protein + DNA
Crystal structure of the guide-strand-containing argonaute protein silencing complex
3DLH: “Crystal structure of the guide-strand-containing argonaute protein silencing complex”. X-ray diffraction, 2 ligands (MG, PO4), 16 pockets (best druggability 0.78). MolNFT v1 #61436 on GenesisL1: 3D structure, binding sites and…
- PDB
- 3DLH
- Type
- protein + DNA
- Length
- 1,367 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argonaute; DNA (5'- D(DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*D…
- UniProt
- Q746M7
- Ligands
- MG, PO4
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute | protein | 673 | 28% helix, 30% strand | Q746M7 |
| B | Argonaute | protein | 666 | 29% helix, 29% strand | Q746M7 |
| X | DNA (5'- D(DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*D GP*DTP*DAP*DTP*DAP*DGP*DT)-3') | dna | 16 | — | — |
| Y | DNA (5'- D(DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DAP*DGP*DGP*DTP*DTP*D GP*DTP*DAP*DTP*DAP*DGP*DT)-3') | dna | 12 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 3 copies · chains A, X, B, Y
- PO4 · Phosphate ion · ion · 2 copies · chains A, X
- ACY · Acetic acid · additive · 2 copies · chains B
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1107 | 0.78 | 0.80 | 92 | empty |
| 2 | 606 | 0.72 | 0.80 | 78 | empty |
| 3 | 99 | 0.68 | 0.92 | 27 | empty |
| 4 | 419 | 0.65 | 0.79 | 51 | ACY |
| 5 | 429 | 0.58 | 0.75 | 37 | empty |
Interfaces
3 interfaces between chains.
- A–X · 2055 Ų buried · 50 hydrogen bonds · protein-nucleic
- B–Y · 1685 Ų buried · 46 hydrogen bonds · protein-nucleic
- A–B · 731 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3DLH · Crystal structure of the guide-strand-containing Argonaute protein 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 3DLH · PDBe 3DLH · UniProt Q746M7
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