MolNFT v1 · #113215 · protein + RNA
Human ERF1 and the hcmv nascent peptide in the translation termination complex
5A8L · 28S ribosomal RNA: “Human ERF1 and the hcmv nascent peptide in the translation termination complex”. Electron microscopy, 20 pockets (best druggability 0.82). MolNFT v1 #113215 on GenesisL1: 3D structure, binding sites and pockets…
- 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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