Research workbench

Paromomycin bound to a leishmanial ribosomal a-site

Analyse Paromomycin bound to a leishmanial ribosomal a-site in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4ZC7
Type: RNA
Length: 82 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA duplex
Ligands: PAR
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	RNA duplex	rna	21	—	—
B, D	RNA duplex	rna	20	—	—

Ligands and binding sites

PAR · Paromomycin · ligand · 2 copies · chains A, B, C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	582	0.59	0.73	28	PAR
2	567	0.59	0.74	28	empty
3	139	0.47	0.78	18	empty

Interfaces

5 interfaces between chains.

A–B · 964 Å² buried · 90 hydrogen bonds · nucleic-nucleic
C–D · 959 Å² buried · 96 hydrogen bonds · nucleic-nucleic
B–C · 95 Å² buried · 2 hydrogen bonds · nucleic-nucleic
A–D · 86 Å² buried · 1 hydrogen bond · nucleic-nucleic
A–C · 80 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

4ZC7 · Paromomycin bound to a leishmanial ribosomal A-site · 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 4ZC7 · PDBe 4ZC7

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