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Crystal structure of cag repeats with synthetic CMBL3B compound

Analyse Crystal structure of cag repeats with synthetic CMBL3B compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6QIT
Type: RNA
Length: 32 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*GP*CP*AP*GP*CP*AP*GP*C)-3')
Ligands: J48
Pockets: 1 · best druggability 0.63

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA (5'-R(GPCPAPGPCPAPGPC)-3')	rna	8	—	—

Ligands and binding sites

J48 · CMBL3a · ligand · 4 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	639	0.63	0.75	20	J48

Interfaces

6 interfaces between chains.

C–D · 299 Å² buried · 13 hydrogen bonds · nucleic-nucleic
A–B · 298 Å² buried · 13 hydrogen bonds · nucleic-nucleic
A–C · 105 Å² buried · 1 hydrogen bond · nucleic-nucleic
B–D · 100 Å² buried · 2 hydrogen bonds · nucleic-nucleic
A–D · 36 Å² buried · 1 hydrogen bond · nucleic-nucleic

Compared structures

6QIT · Crystal structure of CAG repeats with synthetic CMBL3b compound · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 6QIT · PDBe 6QIT

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