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Structure of the B. subtilis cobalamin riboswitch

Analyse Structure of the B. subtilis cobalamin riboswitch in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6VMY
Type: RNA
Length: 148 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.25
Source: Bacillus subtilis
Molecule: B. subtilis cobalamin riboswitch
Ligands: NCO, B1Z, MG
Pockets: 9 · best druggability 0.66

Structure

x-ray diffraction · resolution 3.25 · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	B. subtilis cobalamin riboswitch	rna	148	—	—

Ligands and binding sites

NCO · Cobalt hexammine(iii) · ligand · 7 copies · chains A
B1Z · Adenosylcobalamin · ligand · chains A
MG · Magnesium ion · metal · 12 copies · chains A

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

Pockets

9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	455	0.66	0.79	40	MG, NCO
2	234	0.56	0.80	20	empty
3	277	0.54	0.77	19	MG
4	312	0.50	0.74	20	MG
5	117	0.40	0.77	13	empty

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

6VMY · Structure of the B. subtilis cobalamin riboswitch · 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 6VMY · PDBe 6VMY

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