MolNFT v1 · #61432 · protein + DNA
Crystal structure of the guide-strand-containing argonaute protein silencing complex
3DLB: “Crystal structure of the guide-strand-containing argonaute protein silencing complex”. X-ray diffraction, 17 pockets (best druggability 0.78). MolNFT v1 #61432 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3DLB
- Type
- protein + DNA
- Length
- 1,260 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*DA)-3')
- UniProt
- Q746M7
- Pockets
- 17 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 28% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute | protein | 637 | 30% helix, 31% strand | Q746M7 |
| B | Argonaute | protein | 614 | 27% helix, 30% strand | Q746M7 |
| X | DNA (5'- D(*DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DA)-3') | dna | 5 | — | — |
| Y | DNA (5'- D(*DTP*DGP*DAP*DGP*DGP*DTP*DAP*DGP*DTP*DA)-3') | dna | 4 | — | — |
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 791 | 0.78 | 0.82 | 65 | empty |
| 2 | 725 | 0.72 | 0.78 | 65 | empty |
| 3 | 654 | 0.65 | 0.75 | 67 | empty |
| 4 | 288 | 0.64 | 0.81 | 37 | empty |
| 5 | 253 | 0.61 | 0.80 | 43 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1907 Ų buried · 25 hydrogen bonds · protein-protein
- A–X · 763 Ų buried · 13 hydrogen bonds · protein-nucleic
- B–Y · 683 Ų buried · 10 hydrogen bonds · protein-nucleic
- B–X · 84 Ų buried · 2 hydrogen bonds · protein-nucleic
- A–Y · 81 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 3DLB · 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 3DLB · PDBe 3DLB · UniProt Q746M7
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