MolNFT v1 · #177294 · RNA

RNA duplex containing C-au-C base pair

7EDU · RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3'): “RNA duplex containing C-au-C base pair”. X-ray diffraction, 1 ligand (AU), 2 pockets (best druggability 0.49). MolNFT v1 #177294 on GenesisL1: 3D structure, binding sites and…

PDB: 7EDU
Type: RNA
Length: 48 nucleotides
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA (5'-R(*GP*GP*AP*CP*UP*CP*GP*AP*CP*UP*CP*C)-3')
Ligands: AU
Pockets: 2 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	RNA (5'-R(GPGPAPCPUPCPGPAPCPUPCPC)-3')	rna	12	—	—

Ligands and binding sites

AU · Gold ion · metal · 4 copies · chains A, B, C, 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	294	0.49	0.74	17	empty
2	313	0.49	0.73	19	empty

Interfaces

6 interfaces between chains.

A–B · 541 Å² buried · 43 hydrogen bonds · nucleic-nucleic
C–D · 538 Å² buried · 55 hydrogen bonds · nucleic-nucleic
A–C · 109 Å² buried · 2 hydrogen bonds · nucleic-nucleic
B–D · 95 Å² buried · 2 hydrogen bonds · nucleic-nucleic
A–D · 41 Å² buried · 0 hydrogen bonds · nucleic-nucleic

Compared structures

7EDU · RNA duplex containing C-Au-C base pair · 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 7EDU · PDBe 7EDU

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