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Crystal structure of a mutant (C109G,G212C) P4-P6 domain of the group I intron from tetrahymena thermophilia

Analyse Crystal structure of a mutant (C109G,G212C) P4-P6 domain of the group I intron… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1L8V
Type: RNA
Length: 314 nucleotides
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: P4-P6 RNA ribozyme domain
Ligands: MG
Pockets: 10 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	P4-P6 RNA ribozyme domain	rna	157	—	—

Ligands and binding sites

MG · Magnesium ion · metal · 10 copies · chains A, B

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

Pockets

10 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1064	0.78	0.81	70	MG
2	847	0.77	0.81	59	MG
3	356	0.57	0.77	29	empty
4	460	0.55	0.73	23	empty
5	426	0.55	0.74	22	empty

Interfaces

1 interface between chains.

A–B · 925 Å² buried · 34 hydrogen bonds · nucleic-nucleic

Compared structures

1L8V · Crystal Structure of a Mutant (C109G,G212C) P4-P6 Domain of the Group I Intron from… · the same entry in another collection · chain A against A, TM-score 1.00

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Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Elsewhere: RCSB PDB 1L8V · PDBe 1L8V

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