MolNFT v1 · #144784 · protein + RNA
Conformation of methylated ggq in the peptidyl transferase center during translation termination (ptc region)
6C4H · 23S rRNA: “Conformation of methylated ggq in the peptidyl transferase center during translation termination (ptc region)”. Electron microscopy, 1 ligand (MG), 20 pockets (best druggability 0.85). MolNFT v1 #144784 on GenesisL1: 3D…
- 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.
| Volume (ų) | 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 Ų buried · 58 hydrogen bonds · protein-nucleic
- A–D · 2269 Ų buried · 66 hydrogen bonds · protein-nucleic
- A–v · 1422 Ų buried · 35 hydrogen bonds · protein-nucleic
- A–N · 760 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–X · 608 Ų 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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