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Crystal structure analysis of the 16MER gcagncuuaagucugc containing 8- aza-7-deaza-7-ethynyl adenosine

Analyse Crystal structure analysis of the 16MER gcagncuuaagucugc containing 8… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4NFP
Type: RNA
Length: 48 nucleotides
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: GCAG(A7E)CUUAAGUCUGC
Ligands: ARF
Pockets: 2 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	GCAG(A7E)CUUAAGUCUGC	rna	16	—	—

Ligands and binding sites

ARF · Formamide · ligand · 3 copies · chains A, B, C

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

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	221	0.43	0.73	15	ARF
2	95	0.29	0.72	12	ARF

Interfaces

2 interfaces between chains.

B–C · 747 Å² buried · 76 hydrogen bonds · nucleic-nucleic
A–C · 121 Å² buried · 1 hydrogen bond · nucleic-nucleic

Modifications

Observed in the structure: 3 modified (nucleotide modification).

Compared structures

4NFP · Crystal Structure Analysis of the 16mer GCAGNCUUAAGUCUGC containing… · 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 4NFP · PDBe 4NFP

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