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Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA

Analyse Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EEN
Type: RNA
Length: 105 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA/RNA (27-mer)
Ligands: CA
Pockets: 4 · best druggability 0.65

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	DNA/RNA (27-mer)	rna	26	—	—
B	DNA/RNA (27-mer)	rna	27	—	—

Ligands and binding sites

CA · Calcium ion · metal · 33 copies · chains A, C, B, D

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

Pockets

4 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	685	0.65	0.76	50	CA
2	376	0.50	0.72	31	CA
3	117	0.44	0.79	24	CA
4	55	0.31	0.77	11	empty

Interfaces

4 interfaces between chains.

A–B · 536 Å² buried · 1 hydrogen bond · nucleic-nucleic
C–D · 531 Å² buried · 1 hydrogen bond · nucleic-nucleic
B–C · 249 Å² buried · 6 hydrogen bonds · nucleic-nucleic
A–C · 102 Å² buried · 5 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 40 modified (nucleotide modification).

Compared structures

7EEN · Bulged-G motif composed of RNA, DNA and 2'-O-methyl RNA · 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 7EEN · PDBe 7EEN

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