MolNFT v1 · #29141 · RNA

Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G watson-crick base pair

1YZD · RNA 5'-R(*GP*CP*AP*GP*AP*(A5M) P*UP*UP*AP*AP*GP*UP*CP*UP*GP*…: “Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a C-G watson-crick…”. X-ray diffraction, 1 ligand (CA), 1 pocket (best…

PDB: 1YZD
Type: RNA
Length: 48 nucleotides
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA 5'-R(*GP*CP*AP*GP*AP*(A5M) P*UP*UP*AP*AP*GP*UP*CP*UP*GP*C)-3'
Ligands: CA
Pockets: 1 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A, C	RNA 5'-R(GPCPAPGPAP(A5M) PUPUPAPAPGPUPCPUPGPC)-3'	rna	16	—	—

Ligands and binding sites

CA · Calcium ion · metal · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	356	0.51	0.73	21	empty

Interfaces

1 interface between chains.

B–A · 746 Å² buried · 96 hydrogen bonds · nucleic-nucleic

Modifications

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

Compared structures

1YZD · Crystal structure of an RNA duplex containing a site specific 2'-amine substitution at a… · the same entry in another collection · chain C against C, 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 1YZD · PDBe 1YZD

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