MolNFT v1 · #66622 · protein + DNA + RNA
Crystal structure of T. thermophilus argonaute complexed with DNA guide strand and 19-nt RNA target strand with two MG2+ at the cleavage site
3HVR: “Crystal structure of T. thermophilus argonaute complexed with DNA guide strand and 19-nt RNA target strand…”. X-ray diffraction, 2 ligands (MG, PO4), 20 pockets (best druggability 0.80). MolNFT v1 #66622 on GenesisL1: 3D structure…
- PDB
- 3HVR
- Type
- protein + DNA + RNA
- Length
- 1,370 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Argonaute; 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*TP*GP*AP*T P*AP*GP*T)-3'…
- UniProt
- Q746M7
- Ligands
- MG, PO4
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 29% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Argonaute | protein | 660 | 29% helix, 27% strand | Q746M7 |
| B | Argonaute | protein | 657 | 29% helix, 28% strand | Q746M7 |
| C, M | 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*TP*GP*AP*T P*AP*GP*T)-3' | dna | 16 | — | — |
| D | 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP *G)-3' | rna | 11 | — | — |
| N | 5'-R(*UP*AP*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*CP*CP*UP*CP *G)-3' | rna | 10 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, M, D, N
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1129 | 0.80 | 0.82 | 55 | empty |
| 2 | 1194 | 0.78 | 0.81 | 60 | empty |
| 3 | 578 | 0.71 | 0.79 | 70 | empty |
| 4 | 95 | 0.65 | 0.90 | 26 | empty |
| 5 | 124 | 0.64 | 0.88 | 26 | empty |
Interfaces
7 interfaces between chains.
- A–B · 2202 Ų buried · 36 hydrogen bonds · protein-protein
- A–C · 1362 Ų buried · 36 hydrogen bonds · protein-nucleic
- B–M · 1350 Ų buried · 31 hydrogen bonds · protein-nucleic
- A–D · 642 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–D · 547 Ų buried · 43 hydrogen bonds · nucleic-nucleic
Compared structures
- 3HVR · Crystal structure of T. thermophilus Argonaute complexed with DNA guide strand and 19-nt… · 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 3HVR · PDBe 3HVR · UniProt Q746M7
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