MolNFT v1 · #91291 · RNA

Crystal structure of the bacterial ribosomal decoding site in complex with sisomicin (P21212 form)

4F8V · RNA (5'- R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP…: “Crystal structure of the bacterial ribosomal decoding site in complex with sisomicin (P21212 form)”. X-ray diffraction, 1 ligand (SIS), 1 pocket (best druggability…

PDB: 4F8V
Type: RNA
Length: 42 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'- R(P*GP*CP*GP*UP*CP*AP*CP*AP*CP*CP*GP*GP*UP*GP*AP*AP*GP*UP*CP*GP*C)- 3')
Ligands: SIS
Pockets: 1 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA (5'- R(PGPCPGPUPCPAPCPAPCPCPGPGPUPGPAPAPGPUPCPGP*C)- 3')	rna	21	—	—

Ligands and binding sites

SIS · (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(aminomethyl)-3,4-dihydro-2H-pyran-2-yl]oxy}-2-hydroxycyclohexyl 3-deoxy-4-C-methyl-3-(methylamino)-beta-L-arabinopyranoside · ligand · 2 copies · chains A, B

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	344	0.51	0.74	23	empty

Interfaces

1 interface between chains.

A–B · 977 Å² buried · 93 hydrogen bonds · nucleic-nucleic

Compared structures

4F8V · Crystal structure of the bacterial ribosomal decoding site in complex with sisomicin… · 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 4F8V · PDBe 4F8V

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