MolNFT v1 · #139759 · protein + DNA + RNA
Crystal structure of T. thermophilus argonaute protein complexed with a bulge 9'U10' on the target strand
5XPA · Uncharacterized protein ago: “Crystal structure of T. thermophilus argonaute protein complexed with a bulge 9'U10' on the target strand”. X-ray diffraction, 1 ligand (MG), 9 pockets (best druggability 0.81). MolNFT v1 #139759 on…
- PDB
- 5XPA
- Type
- protein + DNA + RNA
- Length
- 718 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein ago; DNA (5'- D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*…
- UniProt
- Q746M7
- Ligands
- MG
- Pockets
- 9 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 28% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein ago | protein | 679 | 28% helix, 29% strand | Q746M7 |
| C | DNA (5'- D(P*TP*GP*AP*GP*GP*TP*AP*GP*TP*AP*GP*GP*TP*TP*GP*TP*AP*TP*AP*GP*T)- 3') | dna | 21 | — | — |
| D | RNA (5'- R(P*AP*UP*AP*CP*AP*AP*CP*CP*GP*UP*UP*CP*UP*AP*CP*UP*CP*CP*G)-3') | rna | 18 | — | — |
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
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1148 | 0.81 | 0.83 | 78 | empty |
| 2 | 93 | 0.63 | 0.90 | 21 | empty |
| 3 | 187 | 0.54 | 0.79 | 30 | empty |
| 4 | 160 | 0.50 | 0.78 | 36 | empty |
| 5 | 67 | 0.44 | 0.82 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–C · 1576 Ų buried · 42 hydrogen bonds · protein-nucleic
- C–D · 818 Ų buried · 61 hydrogen bonds · nucleic-nucleic
- A–D · 649 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 5XPA · Crystal structure of T. thermophilus Argonaute protein complexed with a bulge 9'U10' 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 5XPA · PDBe 5XPA · UniProt Q746M7
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