MolNFT v1 · #177259 · RNA

RNA duplex containing C-a base pair

7ECM · RNA (5'-R(*GP*GP*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3'): “RNA duplex containing C-a base pair”. X-ray diffraction, 1 ligand (BA), 3 pockets (best druggability 0.46). MolNFT v1 #177259 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 7ECM
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*GP*CP*CP*CP*GP*GP*AP*CP*CP*C)-3')
Ligands: BA
Pockets: 3 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain.

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

Ligands and binding sites

BA · Barium ion · metal · 9 copies · chains A, B, C, D

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

Pockets

3 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	260	0.46	0.73	21	BA
2	262	0.45	0.73	22	BA
3	58	0.35	0.79	12	empty

Interfaces

5 interfaces between chains.

A–B · 587 Å² buried · 58 hydrogen bonds · nucleic-nucleic
C–D · 568 Å² buried · 54 hydrogen bonds · nucleic-nucleic
B–C · 116 Å² buried · 3 hydrogen bonds · nucleic-nucleic
A–D · 89 Å² buried · 2 hydrogen bonds · nucleic-nucleic
A–C · 53 Å² buried · 1 hydrogen bond · nucleic-nucleic

Compared structures

7ECM · RNA duplex containing C-A 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 7ECM · PDBe 7ECM

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