Research workbench
X-ray structure of roquin roq domain in complex with a selex-derived hexa-loop RNA motif
Analyse X-ray structure of roquin roq domain in complex with a selex-derived hexa-loop… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F5F
- Type
- protein + RNA
- Length
- 684 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Roquin-1; RNA (5'- R(P*UP*GP*AP*CP*UP*GP*CP*GP*UP*UP*UP*UP*AP*GP*GP*AP*GP*UP*UP*A)-3')
- UniProt
- Q4VGL6
- Pockets
- 10 · best druggability 0.80
Structure
x-ray diffraction · 3 distinct chains · 62% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Roquin-1 | protein | 152 | 62% helix, 10% strand | Q4VGL6 |
| B, D, F, H | RNA (5'- R(P*UP*GP*AP*CP*UP*GP*CP*GP*UP*UP*UP*UP*AP*GP*GP*AP*GP*UP*UP*A)-3') | rna | 20 | — | — |
| G | Roquin-1 | protein | 148 | 61% helix, 10% strand | Q4VGL6 |
Pockets
10 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 889 | 0.80 | 0.83 | 53 | empty |
| 2 | 729 | 0.79 | 0.84 | 71 | empty |
| 3 | 858 | 0.77 | 0.81 | 63 | empty |
| 4 | 268 | 0.68 | 0.84 | 31 | empty |
| 5 | 260 | 0.64 | 0.82 | 28 | empty |
Interfaces
13 interfaces between chains.
- E–F · 1088 Ų buried · 29 hydrogen bonds · protein-nucleic
- C–D · 881 Ų buried · 26 hydrogen bonds · protein-nucleic
- A–B · 869 Ų buried · 30 hydrogen bonds · protein-nucleic
- G–H · 868 Ų buried · 24 hydrogen bonds · protein-nucleic
- C–E · 440 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 5F5F · X-ray structure of Roquin ROQ domain in complex with a Selex-derived hexa-loop RNA motif · the same entry in another collection · chain H against H, TM-score 1.00
- Q4VGL6 · AlphaFold monomer V2.0 prediction for roquin-1 (Q4VGL6) · a predicted model of the same protein · chain G against A, TM-score 0.99
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 Q4VGL6
- Elsewhere: RCSB PDB 5F5F · PDBe 5F5F · UniProt Q4VGL6
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