MolNFT v1 · #104684 · protein + RNA
X-ray structure of the roq domain from murine roquin-1 in complex with a 23-mer TNF-cde RNA
4QI2: “X-ray structure of the roq domain from murine roquin-1 in complex with a 23-mer TNF-cde RNA”. X-ray diffraction, 9 pockets (best druggability 0.63). MolNFT v1 #104684 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4QI2
- Type
- protein + RNA
- Length
- 686 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Roquin-1; RNA (5'- R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP*…
- UniProt
- Q4VGL6
- Pockets
- 9 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 61% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Roquin-1 | protein | 153 | 61% helix, 10% strand | Q4VGL6 |
| C | Roquin-1 | protein | 152 | 62% helix, 11% strand | Q4VGL6 |
| D | Roquin-1 | protein | 154 | 61% helix, 10% strand | Q4VGL6 |
| E | RNA (5'- R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP* G)-3') | rna | 19 | — | — |
| F, H | RNA (5'- R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP* G)-3') | rna | 18 | — | — |
| G | RNA (5'- R(*AP*CP*AP*UP*GP*UP*UP*UP*UP*CP*UP*GP*UP*GP*AP*AP*AP*AP*CP*GP*GP*AP* G)-3') | rna | 19 | — | — |
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 230 | 0.63 | 0.83 | 32 | empty |
| 2 | 107 | 0.63 | 0.88 | 19 | empty |
| 3 | 290 | 0.63 | 0.81 | 30 | empty |
| 4 | 273 | 0.61 | 0.80 | 28 | empty |
| 5 | 304 | 0.51 | 0.73 | 34 | empty |
Interfaces
7 interfaces between chains.
- C–G · 953 Ų buried · 28 hydrogen bonds · protein-nucleic
- D–H · 952 Ų buried · 36 hydrogen bonds · protein-nucleic
- A–E · 804 Ų buried · 28 hydrogen bonds · protein-nucleic
- B–F · 803 Ų buried · 27 hydrogen bonds · protein-nucleic
- A–C · 442 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 4QI2 · X-ray structure of the ROQ domain from murine Roquin-1 in complex with a 23-mer Tnf-CDE… · 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 C against A, TM-score 0.98
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 4QI2 · PDBe 4QI2 · UniProt Q4VGL6
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