MolNFT v1 · #46914 · RNA

L1 ribozyme ligase circular adduct

2OIU · L1 ribozyme RNA ligase: “L1 ribozyme ligase circular adduct”. X-ray diffraction, 1 ligand (MG), 4 pockets (best druggability 0.55). MolNFT v1 #46914 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2OIU
Type: RNA
Length: 142 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: L1 ribozyme RNA ligase
Ligands: MG
Pockets: 4 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
P, Q	L1 ribozyme RNA ligase	rna	71	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 7 copies · chains Q

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

Pockets

4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	464	0.55	0.73	29	empty
2	156	0.36	0.72	14	MG
3	116	0.33	0.72	15	empty
4	54	0.23	0.73	11	empty

Interfaces

1 interface between chains.

P–Q · 578 Å² buried · 27 hydrogen bonds · nucleic-nucleic

Compared structures

2OIU · L1 Ribozyme Ligase circular adduct · the same entry in another collection · chain P against P, 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 2OIU · PDBe 2OIU

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