MolNFT v1 · #16426 · RNA

Crosslinked hammerhead ribozyme initial state

1NYI · 5'-R(P*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3': “Crosslinked hammerhead ribozyme initial state”. X-ray diffraction, 2 ligands (G, CO), 1 pocket (best druggability 0.30). MolNFT v1 #16426 on GenesisL1: 3D structure…

PDB: 1NYI
Type: RNA
Length: 40 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 5'-R(P*GP*UP*GP*GP*UP*CP*UP*GP*AP*UP*GP*AP*GP*GP*CP*C)-3'…
Ligands: G, CO
Pockets: 1 · best druggability 0.30

Structure

x-ray diffraction · 2 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	5'-R(PGPUPGPGPUPCPUPGPAPUPGPAPGPGPCPC)-3'	rna	16	—	—
B	5'-R(GPCPCPGPAPAPAPCPUPCPGPUPAPAPGPAPGPUP CPAPCPCPAPC)-3'	rna	24	—	—

Ligands and binding sites

G · Guanosine-5'-monophosphate · ligand · chains A, B
CO · Cobalt (II) ion · metal · 4 copies · chains A, B

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	88	0.30	0.73	10	empty

Interfaces

1 interface between chains.

A–B · 1000 Å² buried · 90 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

1NYI · Crosslinked Hammerhead Ribozyme Initial State · the same entry in another collection · chain B against B, 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 1NYI · PDBe 1NYI

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