MolNFT v1 · #186473 · RNA

PREQ1-1 (type-1) riboswitch in complex with tandem stacked metabolites

7REX · RNA (34-mer): “PREQ1-1 (type-1) riboswitch in complex with tandem stacked metabolites”. X-ray diffraction, 2 ligands (PRF, MG), 3 pockets (best druggability 0.71). MolNFT v1 #186473 on GenesisL1: 3D structure, binding sites and…

PDB: 7REX
Type: RNA
Length: 97 nucleotides
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (34-mer)
Ligands: PRF, MG
Pockets: 3 · best druggability 0.71

Structure

x-ray diffraction · 3 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA (34-mer)	rna	34	—	—
B	RNA (34-mer)	rna	33	—	—
C	RNA (34-mer)	rna	30	—	—

Ligands and binding sites

PRF · 7-deaza-7-aminomethyl-guanine · ligand · 6 copies · chains A, B, C
MG · Magnesium ion · metal · 4 copies · chains A, C

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	944	0.71	0.77	50	PRF
2	315	0.59	0.78	19	PRF
3	150	0.39	0.74	16	empty

Interfaces

2 interfaces between chains.

A–B · 216 Å² buried · 6 hydrogen bonds · nucleic-nucleic
A–C · 102 Å² buried · 1 hydrogen bond · nucleic-nucleic

Compared structures

7REX · PreQ1-1 (type-1) riboswitch in complex with tandem stacked metabolites · 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 7REX · PDBe 7REX

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