MolNFT v1 · #139765 · protein + DNA + RNA
Crystal structure of T. thermophilus argonaute protein complexed with a bulge 6'U7' on the target strand
5XPG · Uncharacterized protein: “Crystal structure of T. thermophilus argonaute protein complexed with a bulge 6'U7' on the target strand”. X-ray diffraction, 2 ligands (MG, SO4), 8 pockets (best druggability 0.81). MolNFT v1 #139765 on…
- PDB
- 5XPG
- Type
- protein + DNA + RNA
- Length
- 721 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*T P*A…
- UniProt
- Q746M7
- Ligands
- MG, SO4
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 684 | 29% helix, 29% strand | Q746M7 |
| C | 5'-D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*T P*A P*GP*T)-3' | dna | 21 | — | — |
| G | 5'-R(*UP*AP*U*AP*CP*AP*AP*CP*CP*UP*AP*CP*AP*UP*AP*CP*CP*UP* cp* G)-3' | rna | 16 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 897 | 0.81 | 0.83 | 57 | MG |
| 2 | 196 | 0.65 | 0.85 | 31 | empty |
| 3 | 192 | 0.62 | 0.83 | 32 | empty |
| 4 | 128 | 0.53 | 0.82 | 23 | empty |
| 5 | 95 | 0.51 | 0.83 | 22 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1892 Ų buried · 52 hydrogen bonds · protein-nucleic
- A–G · 859 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–G · 773 Ų buried · 67 hydrogen bonds · nucleic-nucleic
Compared structures
- 5XPG · Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 6'U7' on… · 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 5XPG · PDBe 5XPG · UniProt Q746M7
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