Research workbench
Crystal structure of the C-terminal lobe of a budding yeast argonaute
Analyse Crystal structure of the C-terminal lobe of a budding yeast argonaute in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5THE
- Type
- protein + RNA
- Length
- 2,077 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Uncharacterized protein; RNA (5'-R(P*UP*AP*AP*AP*AP*AP*AP*A)-3')
- UniProt
- A7TMA9
- Pockets
- 20 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Uncharacterized protein | protein | 511 | 30% helix, 24% strand | A7TMA9 |
| B, D, F, H | RNA (5'-R(P*UP*AP*AP*AP*AP*AP*AP*A)-3') | rna | 7 | — | — |
| C | Uncharacterized protein | protein | 510 | 31% helix, 24% strand | A7TMA9 |
| E, G | Uncharacterized protein | protein | 514 | 30% helix, 24% strand | A7TMA9 |
Pockets
20 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 672 | 0.70 | 0.78 | 48 | empty |
| 2 | 556 | 0.69 | 0.79 | 67 | empty |
| 3 | 426 | 0.66 | 0.79 | 59 | empty |
| 4 | 328 | 0.55 | 0.76 | 36 | empty |
| 5 | 175 | 0.50 | 0.78 | 26 | empty |
Interfaces
9 interfaces between chains.
- C–D · 989 Ų buried · 29 hydrogen bonds · protein-nucleic
- E–F · 970 Ų buried · 29 hydrogen bonds · protein-nucleic
- A–B · 962 Ų buried · 28 hydrogen bonds · protein-nucleic
- G–H · 930 Ų buried · 28 hydrogen bonds · protein-nucleic
- A–E · 783 Ų buried · 13 hydrogen bonds · protein-protein
Compared structures
- 5THE · Crystal structure of the C-terminal lobe of a budding yeast Argonaute · 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 A7TMA9
- Elsewhere: RCSB PDB 5THE · PDBe 5THE · UniProt A7TMA9
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