Research workbench
Crystal structure of the roq domain of human roquin in complex with the TNF23 RNA duplex
Analyse Crystal structure of the roq domain of human roquin in complex with the TNF23… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QIK
- Type
- protein + RNA
- Length
- 635 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Roquin-1; 5'-R(*AP*C*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP* CP*GP*GP*AP*G)-3'
- UniProt
- Q5TC82
- Ligands
- CL
- Pockets
- 7 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 67% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Roquin-1 | protein | 302 | 66% helix, 3% strand | Q5TC82 |
| B | Roquin-1 | protein | 297 | 68% helix, 3% strand | Q5TC82 |
| C | 5'-R(*AP*C*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP* CP*GP*GP*AP*G)-3' | rna | 18 | — | — |
| D | 5'-R(*AP*C*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP* CP*GP*GP*AP*G)-3' | rna | 18 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.74 | 0.79 | 63 | empty |
| 2 | 733 | 0.72 | 0.78 | 51 | empty |
| 3 | 80 | 0.40 | 0.78 | 17 | empty |
| 4 | 135 | 0.39 | 0.74 | 13 | empty |
| 5 | 127 | 0.38 | 0.74 | 23 | empty |
Interfaces
6 interfaces between chains.
- C–D · 847 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- A–B · 519 Ų buried · 6 hydrogen bonds · protein-protein
- A–D · 375 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 296 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–C · 250 Ų buried · 9 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 12 modified (engineered).
Compared structures
- 4QIK · Crystal structure of the ROQ domain of human Roquin in complex with the TNF23 RNA duplex · the same entry in another collection · chain A against A, TM-score 1.00
- Q5TC82 · AlphaFold monomer V2.0 prediction for roquin-1 (Q5TC82) · a predicted model of the same protein · chain B against A, TM-score 0.94
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 Q5TC82
- Elsewhere: RCSB PDB 4QIK · PDBe 4QIK · UniProt Q5TC82
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