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RNA 10MER duplex with two 2'-5'-linkages

Analyse RNA 10MER duplex with two 2'-5'-linkages in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4MSB
Type: RNA
Length: 60 nucleotides
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA 10MER duplex with two 2'-5'-linkages
Ligands: SR
Pockets: 3 · best druggability 0.47

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F	RNA 10MER duplex with two 2'-5'-linkages	rna	10	—	—

Ligands and binding sites

SR · Strontium ion · metal · 7 copies · chains B, C, D, F, E

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

Pockets

3 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	256	0.47	0.74	18	SR
2	219	0.44	0.73	17	SR
3	164	0.43	0.75	15	empty

Interfaces

5 interfaces between chains.

E–F · 548 Å² buried · 54 hydrogen bonds · nucleic-nucleic
A–B · 544 Å² buried · 55 hydrogen bonds · nucleic-nucleic
C–D · 530 Å² buried · 55 hydrogen bonds · nucleic-nucleic
A–C · 100 Å² buried · 0 hydrogen bonds · nucleic-nucleic
B–D · 73 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

4MSB · RNA 10mer duplex with two 2'-5'-linkages · 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 4MSB · PDBe 4MSB

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