MolNFT v1 · #135956 · RNA

RNA primer-template complex with guanosine dinucleotide P(5')G(3') P(5')G ligand

5UEF · RNA (5'-R(*(LCC)P*(LCC)P*(LCC) P*GP*AP*CP*UP*UP*AP*AP*GP*UP*…: “RNA primer-template complex with guanosine dinucleotide P(5')G(3') P(5')G ligand”. X-ray diffraction, 1 pocket (best druggability 0.46). MolNFT v1 #135956 on GenesisL1…

PDB: 5UEF
Type: RNA
Length: 32 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*(LCC)P*(LCC)P*(LCC) P*GP*AP*CP*UP*UP*AP*AP*GP*UP*CP*G)-3'); RNA…
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	RNA (5'-R((LCC)P(LCC)P(LCC) PGPAPCPUPUPAPAPGPUPCPG)-3')	rna	14	—	—
C, D	RNA (5'-R(PGPG)-3')	rna	2	—	—

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	271	0.46	0.72	20	empty

Interfaces

5 interfaces between chains.

A–B · 573 Å² buried · 57 hydrogen bonds · nucleic-nucleic
B–C · 138 Å² buried · 13 hydrogen bonds · nucleic-nucleic
A–D · 138 Å² buried · 11 hydrogen bonds · nucleic-nucleic
B–D · 115 Å² buried · 3 hydrogen bonds · nucleic-nucleic
A–C · 110 Å² buried · 4 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 6 modified (nucleotide modification).

Compared structures

5UEF · RNA primer-template complex with guanosine dinucleotide p(5')G(3')p(5')G ligand · 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 5UEF · PDBe 5UEF

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