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Conformation of methylated ggq in the peptidyl transferase center during translation termination (ptc region)

Analyse Conformation of methylated ggq in the peptidyl transferase center during… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6C4H
Type: protein + RNA
Length: 832 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 23S rRNA; 50S ribosomal protein L2; 50S ribosomal protein L3; 50S ribosomal protein L16…
UniProt: P60422, P60438, P0ADY7, P0A7L8, P07012
Ligands: MG
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 7 distinct chains · 13% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	23S rRNA	rna	636	—	—
C	50S ribosomal protein L2	protein	47	6% helix, 4% strand	P60422
D	50S ribosomal protein L3	protein	47	9% helix, 0% strand	P60438
N	50S ribosomal protein L16	protein	17	0% helix, 12% strand	P0ADY7
X	50S ribosomal protein L27	protein	10	0% helix, 0% strand	P0A7L8
x	P-site tRNA fmet	rna	12	—	—
v	Peptide chain release factor RF2	protein	63	25% helix, 27% strand	P07012

Ligands and binding sites

MG · Magnesium ion · metal · 34 copies · chains A, C

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

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	638	0.85	0.90	69	MG
2	1185	0.84	0.86	83	MG
3	630	0.84	0.90	59	MG
4	674	0.82	0.87	77	MG
5	854	0.81	0.85	59	MG

Interfaces

11 interfaces between chains.

A–C · 2519 Å² buried · 58 hydrogen bonds · protein-nucleic
A–D · 2269 Å² buried · 66 hydrogen bonds · protein-nucleic
A–v · 1422 Å² buried · 35 hydrogen bonds · protein-nucleic
A–N · 760 Å² buried · 17 hydrogen bonds · protein-nucleic
A–X · 608 Å² buried · 14 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 18 modified (nucleotide modification, nonstandard).

Compared structures

6C4H · Conformation of methylated GGQ in the peptidyl transferase center during translation… · the same entry in another collection · chain v against v, TM-score 1.00
P07012 · AlphaFold monomer V2.0 prediction for peptide chain release factor RF2 (P07012) · a predicted model of the same protein · chain v against A, TM-score 0.91

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P60422
Every structure of UniProt P60438
Every structure of UniProt P0ADY7
Every structure of UniProt P0A7L8
Every structure of UniProt P07012
Elsewhere: RCSB PDB 6C4H · PDBe 6C4H · UniProt P60422 · UniProt P60438 · UniProt P0ADY7 · UniProt P0A7L8 · UniProt P07012

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