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RNA kink-turn motif with 2-aminopurine

Analyse RNA kink-turn motif with 2-aminopurine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7EI8
Type: RNA
Length: 76 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*GP*GP*C)-D(P*(2PR)P*(2PR)P*(2PR)P*(2PR))…
Ligands: CO
Pockets: 1 · best druggability 0.66

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA (5'-R(GPGPC)-D(P(2PR)P(2PR)P(2PR)P(2PR))- R(PAPAPCPCPGPGPGPGPAPGPCP*C)-3')	rna	19	—	—

Ligands and binding sites

CO · Cobalt (II) ion · metal · 14 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	1165	0.66	0.73	59	CO

Interfaces

6 interfaces between chains.

C–D · 1320 Å² buried · 110 hydrogen bonds · nucleic-nucleic
A–B · 1289 Å² buried · 110 hydrogen bonds · nucleic-nucleic
A–D · 165 Å² buried · 4 hydrogen bonds · nucleic-nucleic
B–C · 160 Å² buried · 3 hydrogen bonds · nucleic-nucleic
B–D · 89 Å² buried · 6 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 16 modified (nucleotide modification).

Compared structures

7EI8 · RNA kink-turn motif with 2-aminopurine · 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 7EI8 · PDBe 7EI8

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