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Crystal structure of an RNA dodecamer containing the escherichia COLI shine-dalgarno sequence

Analyse Crystal structure of an RNA dodecamer containing the escherichia COLI… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1SDR
Type: RNA
Length: 48 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*UP*AP*AP*GP*GP*AP*GP*GP*UP*GP*AP*U)- 3'); RNA…
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	RNA (5'-R(UPAPAPGPGPAPGPGPUPGPAPU)- 3')	rna	12	—	—
B, D	RNA (5'-R(APUPCPAPCPCPUPCPCPUPUPA)- 3')	rna	12	—	—

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	333	0.51	0.74	16	empty
2	290	0.49	0.74	17	empty

Interfaces

5 interfaces between chains.

A–B · 576 Å² buried · 57 hydrogen bonds · nucleic-nucleic
C–D · 574 Å² buried · 58 hydrogen bonds · nucleic-nucleic
B–C · 129 Å² buried · 3 hydrogen bonds · nucleic-nucleic
A–C · 126 Å² buried · 3 hydrogen bonds · nucleic-nucleic
A–D · 66 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

1SDR · Crystal structure of an RNA dodecamer containing the escherichia COLI shine-dalgarno… · 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 1SDR · PDBe 1SDR

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