Research workbench
X-ray structure of roquin roq domain in complex with OX40 hexa-loop RNA motif
Analyse X-ray structure of roquin roq domain in complex with OX40 hexa-loop RNA motif in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F5H
- Type
- protein + RNA
- Length
- 342 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Roquin-1; RNA (5'- R(P*CP*CP*AP*CP*AP*CP*CP*GP*UP*UP*CP*UP*AP*GP*GP*UP*GP*CP*UP*GP*G)- 3')
- UniProt
- Q4VGL6
- Pockets
- 5 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 63% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Roquin-1 | protein | 148 | 62% helix, 7% strand | Q4VGL6 |
| B | Roquin-1 | protein | 152 | 63% helix, 7% strand | Q4VGL6 |
| C, D | RNA (5'- R(P*CP*CP*AP*CP*AP*CP*CP*GP*UP*UP*CP*UP*AP*GP*GP*UP*GP*CP*UP*GP*G)- 3') | rna | 21 | — | — |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.75 | 0.85 | 40 | empty |
| 2 | 350 | 0.68 | 0.82 | 32 | empty |
| 3 | 544 | 0.64 | 0.76 | 45 | empty |
| 4 | 66 | 0.56 | 0.89 | 15 | empty |
| 5 | 80 | 0.33 | 0.74 | 11 | empty |
Interfaces
3 interfaces between chains.
- A–C · 843 Ų buried · 19 hydrogen bonds · protein-nucleic
- B–D · 760 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–B · 215 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
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 5F5H · PDBe 5F5H · UniProt Q4VGL6
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