Research workbench
Crystal structure of the roq domain of human roquin in complex with the HMG19 stem-loop RNA
Analyse Crystal structure of the roq domain of human roquin in complex with the HMG19… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4QIL
- Type
- protein + RNA
- Length
- 623 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Roquin-1; 5'-R(*CP*UP*CP*CP*CP*UP*UP*CP*UP*GP*UP*GP*AP*AP*GP*GP*GP*GP *a)-3'
- UniProt
- Q5TC82
- Ligands
- CA
- Pockets
- 11 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Roquin-1 | protein | 299 | 65% helix, 3% strand | Q5TC82 |
| B | Roquin-1 | protein | 292 | 69% helix, 5% strand | Q5TC82 |
| D, C | 5'-R(*CP*UP*CP*CP*CP*UP*UP*CP*UP*GP*UP*GP*AP*AP*GP*GP*GP*GP *a)-3' | rna | 16 | — | — |
Ligands and binding sites
- CA · Calcium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 342 | 0.68 | 0.82 | 33 | empty |
| 2 | 416 | 0.67 | 0.79 | 33 | empty |
| 3 | 278 | 0.66 | 0.82 | 35 | empty |
| 4 | 86 | 0.64 | 0.91 | 17 | empty |
| 5 | 309 | 0.60 | 0.78 | 35 | empty |
Interfaces
5 interfaces between chains.
- A–C · 984 Ų buried · 25 hydrogen bonds · protein-nucleic
- B–D · 975 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–B · 456 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 54 Ų buried · 0 hydrogen bonds · protein-nucleic
- B–C · 50 Ų buried · 0 hydrogen bonds · protein-nucleic
Compared structures
- 4QIL · Crystal structure of the ROQ domain of human Roquin in complex with the Hmg19 stem-loop… · the same entry in another collection · chain B against B, 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 0.95
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 4QIL · PDBe 4QIL · UniProt Q5TC82
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.