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Crystal structure of squash RNA aptamer in complex with dfhbi-1T

Analyse Crystal structure of squash RNA aptamer in complex with dfhbi-1T in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7KVV
Type: RNA
Length: 82 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Squash RNA aptamer bound to dfho
Ligands: GTP, 747, MG
Pockets: 2 · best druggability 0.68

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D	Squash RNA aptamer bound to dfho	rna	82	—	—

Ligands and binding sites

GTP · Guanosine-5'-triphosphate · ligand · chains D
747 · (5Z)-5-[(3,5-difluoro-4-hydroxyphenyl)methylidene]-2-[(E)-(hydroxyimino)methyl]-3-methyl-3,5-dihydro-4H-imidazol-4-one · ligand · chains D
MG · Magnesium ion · metal · 2 copies · chains D

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

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	836	0.68	0.75	43	747
2	151	0.37	0.73	14	empty

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

7KVV · Crystal structure of Squash RNA aptamer in complex with DFHBI-1T · the same entry in another collection · chain D against D, 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 7KVV · PDBe 7KVV

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