MolNFT v1 · #135623 · protein + RNA
Structural basis of co-translational quality control by arfa and RF2 bound to ribosome
5U4J · 16S rRNA: “Structural basis of co-translational quality control by arfa and RF2 bound to ribosome”. Electron microscopy, 20 pockets (best druggability 0.86). MolNFT v1 #135623 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5U4J
- Type
- protein + RNA
- Length
- 863 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA; 23S rRNA; 30S ribosomal protein S3; 30S ribosomal protein S4; 30S ribosomal…
- UniProt
- P0A7V3, P0A7V8, P0A7W1, P0A7S3, P07012, P36675
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 10 distinct chains · 23% helix, 28% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a | 16S rRNA | rna | 307 | — | — |
| A | 23S rRNA | rna | 11 | — | — |
| c | 30S ribosomal protein S3 | protein | 21 | 0% helix, 48% strand | P0A7V3 |
| d | 30S ribosomal protein S4 | protein | 65 | 42% helix, 0% strand | P0A7V8 |
| e | 30S ribosomal protein S5 | protein | 136 | 26% helix, 41% strand | P0A7W1 |
| z | MRNA | rna | 6 | — | — |
| x | P-site tRNA fmet | rna | 15 | — | — |
| l | 30S ribosomal protein S12 | protein | 123 | 5% helix, 26% strand | P0A7S3 |
| v | Peptide chain release factor 2 | protein | 132 | 33% helix, 34% strand | P07012 |
| w | Alternative ribosome-rescue factor a | protein | 47 | 19% helix, 6% strand | P36675 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 948 | 0.86 | 0.88 | 77 | empty |
| 2 | 899 | 0.86 | 0.88 | 82 | empty |
| 3 | 995 | 0.83 | 0.85 | 94 | empty |
| 4 | 649 | 0.83 | 0.88 | 62 | empty |
| 5 | 419 | 0.78 | 0.87 | 37 | empty |
Interfaces
21 interfaces between chains.
- a–l · 2843 Ų buried · 70 hydrogen bonds · protein-nucleic
- a–e · 2114 Ų buried · 48 hydrogen bonds · protein-nucleic
- a–w · 1474 Ų buried · 40 hydrogen bonds · protein-nucleic
- v–w · 1445 Ų buried · 15 hydrogen bonds · protein-protein
- a–d · 905 Ų buried · 24 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 10 modified (nucleotide modification).
Compared structures
- 5U4J · Structural Basis of Co-translational Quality Control by ArfA and RF2 Bound to Ribosome · the same entry in another collection · chain w against w, TM-score 1.00
- P36675 · AlphaFold monomer V2.0 prediction for alternative ribosome-rescue factor a (P36675) · a predicted model of the same protein · chain w against A, TM-score 0.93
- 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 0.86
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 P0A7V3
- Every structure of UniProt P0A7V8
- Every structure of UniProt P0A7W1
- Every structure of UniProt P0A7S3
- Every structure of UniProt P07012
- Every structure of UniProt P36675
- Elsewhere: RCSB PDB 5U4J · PDBe 5U4J · UniProt P0A7V3 · UniProt P0A7V8 · UniProt P0A7W1 · UniProt P0A7S3 · UniProt P07012 · UniProt P36675
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.