MolNFT v1 · #38239 · RNA

Crystal structure of an RNA quadruplex containing inosine- tetrad

2GRB · 5'-R(*(U33)P*GP*IP*GP*GP*U)-3': “Crystal structure of an RNA quadruplex containing inosine- tetrad”. X-ray diffraction, 2 ligands (K, SR). MolNFT v1 #38239 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2GRB
Type: RNA
Length: 45 nucleotides
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*(U33)P*GP*IP*GP*GP*U)-3'
Ligands: K, SR

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, H	5'-R((U33)PGPIPGPGPU)-3'	rna	5	—	—
C, D, E, F, G	5'-R((U33)PGPIPGPGPU)-3'	rna	6	—	—

Ligands and binding sites

K · Potassium ion · metal · 11 copies · chains A, B, C, D, E, F, G, H
SR · Strontium ion · metal · chains B, D

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

Interfaces

23 interfaces between chains.

F–H · 340 Å² buried · 17 hydrogen bonds · nucleic-nucleic
F–G · 319 Å² buried · 17 hydrogen bonds · nucleic-nucleic
B–C · 315 Å² buried · 17 hydrogen bonds · nucleic-nucleic
B–D · 253 Å² buried · 14 hydrogen bonds · nucleic-nucleic
E–H · 247 Å² buried · 16 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 5 modified (nucleotide modification).

Compared structures

2GRB · Crystal Structure of an RNA Quadruplex Containing Inosine-tetrad · 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 2GRB · PDBe 2GRB

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