MolNFT v1 · #88518 · protein + RNA
Regulation of the mammalian elongation cycle by 40S subunit rolling: a eukaryotic-specific ribosome rearrangement
4CXH · 18S rRNA - H44: “Regulation of the mammalian elongation cycle by 40S subunit rolling: a eukaryotic-specific ribosome…”. Electron microscopy, 1 ligand (PHE), 20 pockets (best druggability 0.74). MolNFT v1 #88518 on GenesisL1: 3D…
- PDB
- 4CXH
- Type
- protein + RNA
- Length
- 934 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 18S rRNA - H44; 28S rRNA - H89; Elongation factor 1A; 40S ribosomal protein US12…
- UniProt
- Q9YAV0, P62266
- Ligands
- PHE
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 9 distinct chains · 23% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | 18S rRNA - H44 | rna | 135 | — | — |
| 2 | 28S rRNA - H89 | rna | 50 | — | — |
| A | Elongation factor 1A | protein | 427 | 23% helix, 35% strand | Q9YAV0 |
| X | 40S ribosomal protein US12 | protein | 134 | 24% helix, 29% strand | P62266 |
| Y | Transfer RNA | rna | 76 | — | — |
| a | 18S rRNA - H5-H14 | rna | 48 | — | — |
| b | 18S rRNA - H8 | rna | 17 | — | — |
| c | 28S rRNA - H95 | rna | 19 | — | — |
| x | Messenger RNA | rna | 28 | — | — |
Ligands and binding sites
- PHE · Phenylalanine · ligand · chains A, Y
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.74 | 0.79 | 34 | empty |
| 2 | 694 | 0.74 | 0.81 | 57 | empty |
| 3 | 471 | 0.71 | 0.81 | 47 | PHE |
| 4 | 308 | 0.70 | 0.84 | 37 | empty |
| 5 | 327 | 0.69 | 0.83 | 40 | empty |
Interfaces
13 interfaces between chains.
- A–Y · 1042 Ų buried · 22 hydrogen bonds · protein-nucleic
- A–c · 358 Ų buried · 2 hydrogen bonds · protein-nucleic
- A–a · 314 Ų buried · 6 hydrogen bonds · protein-nucleic
- 1–x · 312 Ų buried · 21 hydrogen bonds · nucleic-nucleic
- a–b · 293 Ų buried · 19 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 11 modified, 2 covalent (nucleotide modification, covalent ligand).
Compared structures
- 4CXH · Regulation of the mammalian elongation cycle by 40S subunit rolling: a… · the same entry in another collection · chain x against x, TM-score 1.00
- Q9YAV0 · AlphaFold monomer V2.0 prediction for elongation factor 1-alpha (Q9YAV0) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9YAV0
- Every structure of UniProt P62266
- Elsewhere: RCSB PDB 4CXH · PDBe 4CXH · UniProt Q9YAV0 · UniProt P62266
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