MolNFT v1 · #104702 · protein + RNA
Crystal structure of the roq domain of human roquin in complex with the TNF23 RNA duplex
4QIK · Roquin-1: “Crystal structure of the roq domain of human roquin in complex with the TNF23 RNA duplex”. X-ray diffraction, 1 ligand (CL), 7 pockets (best druggability 0.74). MolNFT v1 #104702 on GenesisL1: 3D structure, binding sites…
- 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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