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2.9 a crystal structure of streptomycin RNA-aptamer complex

Analyse 2.9 a crystal structure of streptomycin RNA-aptamer complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1NTB
Type: RNA
Length: 40 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'- R(*GP*GP*AP*UP*CP*GP*CP*AP*UP*UP*UP*GP*GP*AP*CP*UP*UP*CP*UP *GP*CP*C)-3'; 5'…
Ligands: SRY, NA, MG
Pockets: 2 · best druggability 0.50

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'- R(GPGPAPUPCPGPCPAPUPUPUPGPGPAPCPUPUPCPUP GPCPC)-3'	rna	22	—	—
B	5'- R(CPGPGPCPAPCPCPAPCPGPGPUPCPGPGPAPUPC)- 3'	rna	18	—	—

Ligands and binding sites

SRY · Streptomycin · ligand · chains A, B
NA · Sodium ion · metal · 2 copies · chains A
MG · Magnesium ion · metal · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	218	0.50	0.76	16	empty
2	54	0.42	0.84	15	SRY

Interfaces

1 interface between chains.

A–B · 1091 Å² buried · 98 hydrogen bonds · nucleic-nucleic

Compared structures

1NTB · 2.9 A crystal structure of Streptomycin RNA-aptamer complex · 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 1NTB · PDBe 1NTB

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