MolNFT v1 · #172292 · RNA

Sarcin-ricin loop RNA from ecoli with a A2670-2'-OCF3 modification

6ZXZ: “Sarcin-ricin loop RNA from ecoli with a A2670-2'-OCF3 modification”. X-ray diffraction, 2 ligands (K, NA), 3 pockets (best druggability 0.43). MolNFT v1 #172292 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6ZXZ
Type: RNA
Length: 78 nucleotides
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Sarcin-ricin loop RNA from ecoli with a A2670-2'-OCF3 modification
Ligands: K, NA
Pockets: 3 · best druggability 0.43

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C	Sarcin-ricin loop RNA from ecoli with a A2670-2'-OCF3 modification	rna	26	—	—

Ligands and binding sites

K · Potassium ion · metal · 4 copies · chains A, B, C
NA · Sodium ion · metal · 4 copies · chains A, B, C

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	186	0.43	0.75	17	K
2	175	0.42	0.75	14	K
3	136	0.36	0.73	15	K

Interfaces

1 interface between chains.

A–C · 312 Å² buried · 12 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 3 modified (nucleotide modification).

Compared structures

6ZXZ · Sarcin-Ricin Loop RNA from Ecoli with a A2670-2'-OCF3 modification · 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 6ZXZ · PDBe 6ZXZ

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