MolNFT v1 · #126046 · RNA

N6-methyladenine is accommodated in a conventional a-U basepair

5LR5 · RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3'): “N6-methyladenine is accommodated in a conventional a-U basepair”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.33). MolNFT v1 #126046 on GenesisL1: 3D…

PDB: 5LR5
Type: RNA
Length: 40 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*GP*GP*(6MZ)P*CP*UP*AP*GP*UP*(CBV)P*C)-3')
Ligands: SO4
Pockets: 1 · best druggability 0.33

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA (5'-R(GPGP(6MZ)PCPUPAPGPUP(CBV)PC)-3')	rna	10	—	—

Ligands and binding sites

SO4 · Sulfate ion · ion · chains C, D

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	76	0.33	0.76	11	empty

Interfaces

5 interfaces between chains.

C–D · 466 Å² buried · 41 hydrogen bonds · nucleic-nucleic
A–B · 466 Å² buried · 49 hydrogen bonds · nucleic-nucleic
B–C · 109 Å² buried · 1 hydrogen bond · nucleic-nucleic
A–C · 101 Å² buried · 0 hydrogen bonds · nucleic-nucleic
A–D · 97 Å² buried · 1 hydrogen bond · nucleic-nucleic

Modifications

Observed in the structure: 8 modified (nucleotide modification).

Compared structures

5LR5 · N6-methyladenine is accommodated in a conventional A-U basepair · 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 5LR5 · PDBe 5LR5

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