MolNFT v1 · #139747 · protein + DNA + RNA
Crystal structure of T. thermophilus argonaute protein complexed with a bulge 6'A7' on the target strand
5XOW · Ttago (D546N): “Crystal structure of T. thermophilus argonaute protein complexed with a bulge 6'A7' on the target strand”. X-ray diffraction, 1 ligand (MG), 10 pockets (best druggability 0.81). MolNFT v1 #139747 on GenesisL1: 3D…
- PDB
- 5XOW
- Type
- protein + DNA + RNA
- Length
- 722 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ttago (D546N); DNA (5'-D(P*(TD) P*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP…
- UniProt
- Q746M7
- Ligands
- MG
- Pockets
- 10 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ttago (D546N) | protein | 684 | 28% helix, 30% strand | Q746M7 |
| C | DNA (5'-D(P*(TD) P*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)-3') | dna | 21 | — | — |
| G | RNA (5'- R(P*UP*AP*CP*AP*AP*CP*CP*UP*AP*CP*UP*AP*AP*CP*CP*UP*CP*G)-3') | rna | 17 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.81 | 0.84 | 56 | empty |
| 2 | 95 | 0.62 | 0.89 | 26 | empty |
| 3 | 122 | 0.55 | 0.83 | 18 | empty |
| 4 | 72 | 0.49 | 0.84 | 16 | empty |
| 5 | 94 | 0.46 | 0.81 | 13 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1979 Ų buried · 54 hydrogen bonds · protein-nucleic
- A–G · 998 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–G · 795 Ų buried · 66 hydrogen bonds · nucleic-nucleic
Compared structures
- 5XOW · Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 6'A7' 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 5XOW · PDBe 5XOW · UniProt Q746M7
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