MolNFT v1 · #165291 · protein + RNA

X-ray structure of roquin roq domain in complex with a UCP3 CDE2 sl RNA motif

6TQA · Roquin-1: “X-ray structure of roquin roq domain in complex with a UCP3 CDE2 sl RNA motif”. X-ray diffraction, 2 ligands (MG, CL), 12 pockets (best druggability 0.67). MolNFT v1 #165291 on GenesisL1: 3D structure, binding sites and…

PDB: 6TQA
Type: protein + RNA
Length: 685 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Roquin-1; RNA (5'- R(P*GP*GP*UP*GP*CP*CP*UP*AP*AP*UP*AP*UP*UP*UP*AP*GP*GP*CP*AP*CP*(CCC)…
EC: 2.3.2.27
UniProt: Q4VGL6
Ligands: MG, CL
Pockets: 12 · best druggability 0.67

Structure

x-ray diffraction · 4 distinct chains · 62% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Roquin-1 (EC 2.3.2.27)	protein	152	63% helix, 7% strand	Q4VGL6
E, F, G, H	RNA (5'- R(PGPGPUPGPCPCPUPAPAPUPAPUPUPUPAPGPGPCPAPCP*(CCC) )-3')	rna	21	—	—
B, D	Roquin-1 (EC 2.3.2.27)	protein	149	60% helix, 7% strand	Q4VGL6
C	Roquin-1 (EC 2.3.2.27)	protein	151	63% helix, 7% strand	Q4VGL6

Ligands and binding sites

MG · Magnesium ion · metal · chains D, H
CL · Chloride ion · ion · 3 copies · chains A, B, F

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

Pockets

12 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	399	0.67	0.80	39	CL
2	112	0.67	0.90	20	MG
3	92	0.66	0.91	17	empty
4	116	0.65	0.89	24	CL
5	118	0.64	0.88	24	empty

Interfaces

11 interfaces between chains.

A–E · 906 Å² buried · 24 hydrogen bonds · protein-nucleic
C–G · 893 Å² buried · 26 hydrogen bonds · protein-nucleic
B–F · 886 Å² buried · 26 hydrogen bonds · protein-nucleic
B–C · 883 Å² buried · 18 hydrogen bonds · protein-protein
A–D · 800 Å² buried · 16 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (nucleotide modification).

Compared structures

6TQA · X-ray structure of Roquin ROQ domain in complex with a UCP3 CDE2 SL RNA motif · 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 B against A, TM-score 0.99

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 6TQA · PDBe 6TQA · UniProt Q4VGL6

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