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X-ray structure of roquin roq domain in complex with a UCP3 CDE1 sl RNA motif

Analyse X-ray structure of roquin roq domain in complex with a UCP3 CDE1 sl RNA motif in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6TQB
Type: protein + RNA
Length: 172 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Roquin-1; RNA (5'- R(P*GP*GP*AP*AP*AP*UP*UP*AP*UP*AP*UP*UP*AP*AP*UP*UP*UP*CP*C)-3')
EC: 2.3.2.27
UniProt: Q4VGL6
Ligands: NA, MG, CL
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 2 distinct chains · 62% helix, 9% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Roquin-1 (EC 2.3.2.27)	protein	153	62% helix, 9% strand	Q4VGL6
B	RNA (5'- R(PGPGPAPAPAPUPUPAPUPAPUPUPAPAPUPUPUPCP*C)-3')	rna	19	—	—

Ligands and binding sites

NA · Sodium ion · metal · 2 copies · chains A, B
MG · Magnesium ion · metal · chains B
CL · Chloride ion · ion · 2 copies · chains A, B
EDO · 1,2-ethanediol · additive · 6 copies · chains A, B

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	104	0.63	0.89	17	empty
2	226	0.53	0.78	21	NA, CL

Interfaces

1 interface between chains.

A–B · 859 Å² buried · 25 hydrogen bonds · protein-nucleic

Compared structures

6TQB · X-ray structure of Roquin ROQ domain in complex with a UCP3 CDE1 SL RNA motif · the same entry in another collection · chain A against A, TM-score 1.00
Q4VGL6 · AlphaFold monomer V2.0 prediction for roquin-1 (Q4VGL6) · a predicted model of the same protein · chain A 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 6TQB · PDBe 6TQB · UniProt Q4VGL6

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