Research workbench
Structure of trbp dsrbd 1 and 2 in complex with a 19 bp siRNA (complex B)
Analyse Structure of trbp dsrbd 1 and 2 in complex with a 19 bp siRNA (complex B) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N8L
- Type
- protein + RNA
- Length
- 197 residues
- Chains
- 3
- Method
- solution nmr
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Risc-loading complex subunit TARBP2; RNA (5'- R(*UP*UP*AP*AP*UP*UP*AP*UP*CP*UP*AP*UP*UP*CP…
- UniProt
- Q15633
- Pockets
- 2 · best druggability 0.61
Structure
solution nmr · 3 distinct chains · 39% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Risc-loading complex subunit TARBP2 | protein | 155 | 39% helix, 28% strand | Q15633 |
| B | RNA (5'- R(*UP*UP*AP*AP*UP*UP*AP*UP*CP*UP*AP*UP*UP*CP*CP*GP*UP*AP*CP*UP*U)- 3') | rna | 21 | — | — |
| C | RNA (5'- R(*GP*UP*AP*CP*GP*GP*AP*AP*UP*AP*GP*AP*UP*AP*AP*UP*UP*AP*AP*UP*U)- 3') | rna | 21 | — | — |
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 717 | 0.61 | 0.73 | 39 | empty |
| 2 | 54 | 0.29 | 0.76 | 9 | empty |
Interfaces
3 interfaces between chains.
- B–C · 949 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- A–C · 900 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–B · 840 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 5N8L · Structure of TRBP dsRBD 1 and 2 in complex with a 19 bp siRNA (Complex B) · the same entry in another collection · chain A against A, TM-score 1.00
- Q15633 · AlphaFold monomer V2.0 prediction for risc-loading complex subunit TARBP2 (Q15633) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q15633
- Elsewhere: RCSB PDB 5N8L · PDBe 5N8L · UniProt Q15633
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