MolNFT v1 · #28878 · RNA

Crystal structure of an RNA duplex containing site specific 2'-amine substitutions at a C-a mismatch

1YRM · DNA/RNA (5'-R(*GP*CP*AP*GP*A)-D(P*(A5M))…: “Crystal structure of an RNA duplex containing site specific 2'-amine substitutions at a C-a mismatch”. X-ray diffraction, 1 ligand (SR), 1 pocket (best druggability 0.41). MolNFT v1 #28878…

PDB: 1YRM
Type: RNA
Length: 48 nucleotides
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA/RNA (5'-R(*GP*CP*AP*GP*A)-D(P*(A5M))- R(P*UP*UP*AP*AP*AP*UP*CP*UP*GP*C)-3')
Ligands: SR
Pockets: 1 · best druggability 0.41

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	DNA/RNA (5'-R(GPCPAPGPA)-D(P(A5M))- R(PUPUPAPAPAPUPCPUPGPC)-3')	rna	16	—	—

Ligands and binding sites

SR · Strontium ion · metal · 2 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	217	0.41	0.72	23	empty

Interfaces

1 interface between chains.

A–B · 730 Å² buried · 71 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

1YRM · Crystal Structure of an RNA duplex containing site specific 2'-amine substitutions at a… · 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 1YRM · PDBe 1YRM

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