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

Analyse Crystal structure of the bacterial ribosomal decoding site in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

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

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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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