MolNFT v1 · #93013 · RNA

Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin (P212121 form)

4GPX · RNA (5'- R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*…: “Crystal structure of the protozoal cytoplasmic ribosomal decoding site in complex with 6'-hydroxysisomicin…”. X-ray diffraction, 1 ligand (6HS), 1 pocket (best…

PDB: 4GPX
Type: RNA
Length: 42 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'- R(*UP*UP*GP*CP*GP*UP*CP*GP*CP*GP*CP*CP*GP*GP*CP*GP*AP*AP*GP*UP*CP*GP* C)-3')
Ligands: 6HS
Pockets: 1 · best druggability 0.53

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

6HS · (1S,2S,3R,4S,6R)-4,6-diamino-3-{[(2S,3R)-3-amino-6-(hydroxymethyl)-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	411	0.53	0.73	27	6HS

Interfaces

1 interface between chains.

A–B · 1005 Å² buried · 91 hydrogen bonds · nucleic-nucleic

Compared structures

4GPX · Crystal structure of the protozoal cytoplasmic 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 4GPX · PDBe 4GPX

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