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Crystal structure of the methyltransferase-ribozyme 1 (with 1-methyl- adenosine)

Analyse Crystal structure of the methyltransferase-ribozyme 1 (with 1-methyl- adenosine) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7Q7X
Type: RNA
Length: 62 nucleotides
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: RNA 1; RNA 2; RNA 3
Ligands: GUN, MG
Pockets: 2 · best druggability 0.63

Structure

x-ray diffraction · 3 distinct chains.

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	RNA 1	rna	14	—	—
B	RNA 2	rna	24	—	—
C	RNA 3	rna	24	—	—

Ligands and binding sites

GUN · Guanine · ligand · chains A, B, C
MG · Magnesium ion · metal · 5 copies · chains B, C, A

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

Pockets

2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	714	0.63	0.74	39	MG
2	266	0.52	0.76	18	empty

Interfaces

3 interfaces between chains.

B–C · 900 Å² buried · 63 hydrogen bonds · nucleic-nucleic
A–C · 662 Å² buried · 28 hydrogen bonds · nucleic-nucleic
A–B · 382 Å² buried · 32 hydrogen bonds · nucleic-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

7Q7X · Crystal structure of the methyltransferase-ribozyme 1 (with 1-methyl-adenosine) · 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 7Q7X · PDBe 7Q7X

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