MolNFT v1 · #103024 · RNA

Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin

4P3S · 5'-R(*UP*UP*GP*CP*GP*UP*CP*CP*CP*GP*(5BU)…: “Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with geneticin”. X-ray diffraction, 1 ligand (GET), 1 pocket (best druggability 0.52). MolNFT v1…

PDB: 4P3S
Type: RNA
Length: 43 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(*UP*UP*GP*CP*GP*UP*CP*CP*CP*GP*(5BU) P*CP*GP*AP*CP*GP*AP*AP*GP*UP*CP*GP*C)-3'
Ligands: GET
Pockets: 1 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-R(UPUPGPCPGPUPCPCPCPGP(5BU) PCPGPAPCPGPAPAPGPUPCPGP*C)-3'	rna	21	—	—
B	5'-R(UPUPGPCPGPUPCPCPCPGP(5BU) PCPGPAPCPGPAPAPGPUPCPGP*C)-3'	rna	22	—	—

Ligands and binding sites

GET · Geneticin · ligand · 3 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	397	0.52	0.73	30	GET

Interfaces

1 interface between chains.

A–B · 971 Å² buried · 90 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 2 modified (nucleotide modification).

Compared structures

4P3S · Crystal structure of the bacterial A1408C-mutant ribosomal decoding site in complex with… · 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 4P3S · PDBe 4P3S

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