Research workbench
Human ERF1 and the hcmv nascent peptide in the translation termination complex
Analyse Human ERF1 and the hcmv nascent peptide in the translation termination complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5A8L
- Type
- protein + RNA
- Length
- 971 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 28S ribosomal RNA; Human 18S ribosomal RNA; 60S ribosomal protein L17; 60S ribosomal…
- UniProt
- P18621, P30050, P36578, P62495
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 9 distinct chains · 35% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 28S ribosomal RNA | rna | 253 | — | — |
| B | Human 18S ribosomal RNA | rna | 67 | — | — |
| D | 60S ribosomal protein L17 | protein | 21 | 14% helix, 29% strand | P18621 |
| G | 60S ribosomal protein L12 | protein | 138 | 24% helix, 0% strand | P30050 |
| H | 60S ribosomal protein L4 | protein | 12 | 0% helix, 0% strand | P36578 |
| P | P-site tRNA | rna | 18 | — | — |
| Q | Eukaryotic release factor ERF1 | protein | 431 | 40% helix, 14% strand | P62495 |
| R | MRNA | rna | 9 | — | — |
| Z | Nascent chain | protein | 22 | 41% helix, 0% strand | — |
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.82 | 0.84 | 89 | empty |
| 2 | 1186 | 0.82 | 0.83 | 85 | empty |
| 3 | 1056 | 0.79 | 0.82 | 89 | empty |
| 4 | 292 | 0.77 | 0.90 | 31 | empty |
| 5 | 362 | 0.73 | 0.84 | 53 | empty |
Interfaces
18 interfaces between chains.
- A–Q · 2843 Ų buried · 53 hydrogen bonds · protein-nucleic
- A–Z · 1013 Ų buried · 10 hydrogen bonds · protein-nucleic
- G–Q · 993 Ų buried · 3 hydrogen bonds · protein-protein
- B–Q · 774 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–G · 677 Ų buried · 6 hydrogen bonds · protein-nucleic
Compared structures
- 5A8L · Human eRF1 and the hCMV nascent peptide in the translation termination complex · the same entry in another collection · chain R against R, TM-score 1.00
- P62495 · AlphaFold monomer V2.0 prediction for eukaryotic peptide chain release factor subunit 1… · a predicted model of the same protein · chain Q against A, TM-score 0.72
- P30050 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L12 (P30050) · a predicted model of the same protein · chain G against A, TM-score 0.70
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 P18621
- Every structure of UniProt P30050
- Every structure of UniProt P36578
- Every structure of UniProt P62495
- Elsewhere: RCSB PDB 5A8L · PDBe 5A8L · UniProt P18621 · UniProt P30050 · UniProt P36578 · UniProt P62495
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