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Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 2)

Analyse Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4P43
Type: RNA
Length: 44 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*UP*CP*GP*UP*CP*GP*AP*CP*GP*AP*AP *GP*UP*CP*GP*C)-3'
Ligands: CA, NA
Pockets: 2 · best druggability 0.61

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-R(UPUPGPCPGPUPCPUPCPGPUPCPGPAPCPGPAPAP GPUPCPGP*C)-3'	rna	21	—	—
B	5'-R(UPUPGPCPGPUPCPUPCPGPUPCPGPAPCPGPAPAP GPUPCPGP*C)-3'	rna	23	—	—

Ligands and binding sites

CA · Calcium ion · metal · 2 copies · chains A, B
NA · Sodium ion · metal · 2 copies · chains A, B

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

Pockets

2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	617	0.61	0.74	30	CA
2	106	0.30	0.72	13	CA

Interfaces

1 interface between chains.

A–B · 962 Å² buried · 99 hydrogen bonds · nucleic-nucleic

Compared structures

4P43 · Crystal structure of the bacterial A1408U-mutant ribosomal decoding site (C2 form 2) · 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 4P43 · PDBe 4P43

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