MolNFT v1 · #167833 · RNA

Transitional unit cell 2 of adenine riboswitch aptamer crystal phase transition upon ligand binding

6VWV · Adenine riboswitch aptamer variant: “Transitional unit cell 2 of adenine riboswitch aptamer crystal phase transition upon ligand binding”. X-ray diffraction, 3 ligands (ADE, MG, K), 4 pockets (best druggability 0.69). MolNFT v1…

PDB: 6VWV
Type: RNA
Length: 142 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Adenine riboswitch aptamer variant
Ligands: ADE, MG, K
Pockets: 4 · best druggability 0.69

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Adenine riboswitch aptamer variant	rna	71	—	—

Ligands and binding sites

ADE · Adenine · ligand · 2 copies · chains A, B
MG · Magnesium ion · metal · 2 copies · chains A, B
K · Potassium ion · metal · chains A, B

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

Pockets

4 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	949	0.69	0.75	37	empty
2	733	0.69	0.77	34	empty
3	405	0.55	0.75	25	ADE
4	261	0.52	0.76	21	empty

Interfaces

1 interface between chains.

A–B · 297 Å² buried · 12 hydrogen bonds · nucleic-nucleic

Compared structures

6VWV · Transitional unit cell 2 of adenine riboswitch aptamer crystal phase transition upon… · 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 6VWV · PDBe 6VWV

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