MolNFT v1 · #180478 · RNA

Spinach variant bound to dfhbi-1T

7L0Z · RNA (69-mer): “Spinach variant bound to dfhbi-1T”. X-ray diffraction, 6 ligands (SPM, 2ZY, NA), 4 pockets (best druggability 0.50). MolNFT v1 #180478 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7L0Z
Type: RNA
Length: 69 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (69-mer)
Ligands: SPM, 2ZY, NA, K, MG, PO4
Pockets: 4 · best druggability 0.50

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
G	RNA (69-mer)	rna	69	—	—

Ligands and binding sites

SPM · Spermine · ligand · 3 copies · chains G
2ZY · (5Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2-methyl-3-(2,2,2-trifluoroethyl)-3,5-dihydro-4H-imidazol-4-one · ligand · chains G
NA · Sodium ion · metal · 2 copies · chains G
K · Potassium ion · metal · 2 copies · chains G
MG · Magnesium ion · metal · chains G
PO4 · Phosphate ion · ion · 2 copies · chains G

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

Pockets

4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	358	0.50	0.73	21	empty
2	132	0.43	0.77	15	2ZY, SPM
3	148	0.41	0.75	13	empty
4	153	0.37	0.72	16	empty

Compared structures

7L0Z · Spinach variant bound to DFHBI-1T · the same entry in another collection · chain G against G, 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 7L0Z · PDBe 7L0Z

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