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Fusibacterium ulcerans ztp riboswitch bound to M-1-pyridinyl aica

Analyse Fusibacterium ulcerans ztp riboswitch bound to M-1-pyridinyl aica in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6WZS
Type: RNA
Length: 122 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fusibacterium ulcerans ztp riboswitch
Ligands: UG4, MG, K
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Fusibacterium ulcerans ztp riboswitch	rna	60	—	—
A	Fusibacterium ulcerans ztp riboswitch	rna	62	—	—

Ligands and binding sites

UG4 · 5-amino-1-(pyridin-3-yl)-1H-imidazole-4-carboxamide · ligand · 2 copies · chains B, A
MG · Magnesium ion · metal · 8 copies · chains B, A
K · Potassium ion · metal · 4 copies · chains B, A

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	515	0.68	0.80	33	K, MG, UG4
2	476	0.67	0.80	30	K, MG, UG4
3	113	0.33	0.73	13	empty

Interfaces

1 interface between chains.

B–A · 598 Å² buried · 29 hydrogen bonds · nucleic-nucleic

Compared structures

6WZS · Fusibacterium ulcerans ZTP riboswitch bound to m-1-pyridinyl AICA · the same entry in another collection · chain B against B, 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 6WZS · PDBe 6WZS

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