MolNFT v1 · #111854 · protein + RNA
Crystal structure of the RC3H2 roq domain in complex with stem-loop and double-stranded forms of RNA
4Z31 · Roquin-2: “Crystal structure of the RC3H2 roq domain in complex with stem-loop and double-stranded forms of RNA”. X-ray diffraction, 2 ligands (UNX, CL), 8 pockets (best druggability 0.77). MolNFT v1 #111854 on GenesisL1: 3D…
- PDB
- 4Z31
- Type
- protein + RNA
- Length
- 646 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Roquin-2; RNA (5'-R(*A)- D(P*UP*GP*UP*UP*CP*UP*GP*UP*GP*AP*AP*CP*AP*C)-3')
- UniProt
- Q9HBD1
- Ligands
- UNX, CL
- Pockets
- 8 · best druggability 0.77
Structure
x-ray diffraction · 5 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Roquin-2 | protein | 293 | 67% helix, 5% strand | Q9HBD1 |
| B | Roquin-2 | protein | 295 | 66% helix, 5% strand | Q9HBD1 |
| C | RNA (5'-R(*A)- D(P*UP*GP*UP*UP*CP*UP*GP*UP*GP*AP*AP*CP*AP*C)-3') | rna | 14 | — | — |
| D | RNA (5'-R(*A)- D(P*UP*GP*UP*UP*CP*UP*GP*UP*GP*AP*AP*CP*AP*C)-3') | rna | 14 | — | — |
| E, F | RNA (5'-R(*A)- D(P*UP*GP*UP*UP*CP*UP*GP*UP*GP*AP*AP*CP*AP*C)-3') | rna | 15 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 827 | 0.77 | 0.81 | 67 | empty |
| 2 | 880 | 0.75 | 0.79 | 62 | empty |
| 3 | 221 | 0.61 | 0.81 | 28 | empty |
| 4 | 94 | 0.53 | 0.84 | 15 | empty |
| 5 | 119 | 0.42 | 0.77 | 17 | empty |
Interfaces
7 interfaces between chains.
- A–F · 819 Ų buried · 25 hydrogen bonds · protein-nucleic
- C–D · 746 Ų buried · 57 hydrogen bonds · nucleic-nucleic
- B–E · 743 Ų buried · 23 hydrogen bonds · protein-nucleic
- B–D · 404 Ų buried · 8 hydrogen bonds · protein-nucleic
- A–D · 313 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 4Z31 · Crystal structure of the RC3H2 ROQ domain in complex with stem-loop and double-stranded… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9HBD1 · AlphaFold monomer V2.0 prediction for roquin-2 (Q9HBD1) · a predicted model of the same protein · chain B 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 Q9HBD1
- Elsewhere: RCSB PDB 4Z31 · PDBe 4Z31 · UniProt Q9HBD1
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