Research workbench
Structure of trbp dsrbd 1 and 2 in complex with a 19 bp siRNA (complex a)
Analyse Structure of trbp dsrbd 1 and 2 in complex with a 19 bp siRNA (complex a) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5N8M
- 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
- 3 · best druggability 0.63
Structure
solution nmr · 3 distinct chains · 42% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Risc-loading complex subunit TARBP2 | protein | 155 | 42% helix, 27% 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
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.63 | 0.74 | 31 | empty |
| 2 | 64 | 0.32 | 0.76 | 11 | empty |
| 3 | 73 | 0.31 | 0.75 | 10 | empty |
Interfaces
3 interfaces between chains.
- B–C · 943 Ų buried · 68 hydrogen bonds · nucleic-nucleic
- A–B · 865 Ų buried · 15 hydrogen bonds · protein-nucleic
- A–C · 802 Ų buried · 13 hydrogen bonds · protein-nucleic
Compared structures
- 5N8M · Structure of TRBP dsRBD 1 and 2 in complex with a 19 bp siRNA (Complex A) · 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 0.91
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 5N8M · PDBe 5N8M · UniProt Q15633
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