MolNFT v1 · #125287 · RNA

Structure of an E.COLI initiator trnafmet A1-U72 variant

5L4O · TRNA (76-mer): “Structure of an E.COLI initiator trnafmet A1-U72 variant”. X-ray diffraction, 1 ligand (NA), 3 pockets (best druggability 0.65). MolNFT v1 #125287 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5L4O
Type: RNA
Length: 76 nucleotides
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: TRNA (76-mer)
Ligands: NA
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	TRNA (76-mer)	rna	76	—	—

Ligands and binding sites

NA · Sodium ion · metal · chains 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	604	0.65	0.76	30	NA
2	336	0.57	0.77	19	empty
3	52	0.33	0.79	9	empty

Modifications

Observed in the structure: 5 modified (nucleotide modification).

Compared structures

5L4O · Structure of an E.coli initiator tRNAfMet A1-U72 variant · 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 5L4O · PDBe 5L4O

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