Research workbench
Mechanism of EIF6 release from the nascent 60S ribosomal subunit
Analyse Mechanism of EIF6 release from the nascent 60S ribosomal subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QKL
- Type
- protein + RNA
- Length
- 3,024 residues
- Chains
- 11
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 26S ribosomal RNA; 60S ribosomal protein L3; 60S ribosomal protein L9; 60S ribosomal…
- UniProt
- P34113, Q54XI5, Q54G86, Q54J69, Q54VN6, P14794, Q551M2, Q9Y3A5, P22685, Q54J50
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 11 distinct chains · 17% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| N | 26S ribosomal RNA | rna | 1158 | — | — |
| A | 60S ribosomal protein L3 | protein | 388 | 10% helix, 24% strand | P34113 |
| B | 60S ribosomal protein L9 | protein | 185 | 17% helix, 32% strand | Q54XI5 |
| E | 60S ribosomal protein L23 | protein | 128 | 5% helix, 32% strand | Q54G86 |
| F | 60S ribosomal protein L10 | protein | 216 | 21% helix, 21% strand | Q54J69 |
| G | 60S ribosomal protein L24 | protein | 53 | 15% helix, 23% strand | Q54VN6 |
| H | Ubiquitin-60S ribosomal protein L40 | protein | 51 | 22% helix, 12% strand | P14794 |
| I | Eukaryotic translation initiation factor 6 | protein | 224 | 22% helix, 16% strand | Q551M2 |
| J | Ribosome maturation protein sbds | protein | 250 | 26% helix, 21% strand | Q9Y3A5 |
| C | 60S acidic ribosomal protein P0 | protein | 205 | 16% helix, 11% strand | P22685 |
| D | 60S ribosomal protein L12 | protein | 166 | 13% helix, 2% strand | Q54J50 |
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 | 1160 | 0.84 | 0.86 | 93 | empty |
| 2 | 915 | 0.84 | 0.87 | 90 | empty |
| 3 | 734 | 0.84 | 0.88 | 73 | empty |
| 4 | 1004 | 0.83 | 0.85 | 75 | empty |
| 5 | 928 | 0.81 | 0.84 | 67 | empty |
Interfaces
23 interfaces between chains.
- N–A · 5942 Ų buried · 114 hydrogen bonds · protein-nucleic
- N–F · 3472 Ų buried · 59 hydrogen bonds · protein-nucleic
- N–J · 2000 Ų buried · 30 hydrogen bonds · protein-nucleic
- N–B · 1903 Ų buried · 31 hydrogen bonds · protein-nucleic
- N–E · 1817 Ų buried · 34 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6QKL · Mechanism of eIF6 release from the nascent 60S ribosomal subunit · the same entry in another collection · chain D against D, TM-score 1.00
- P34113 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L3 (P34113) · 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 P34113
- Every structure of UniProt Q54XI5
- Every structure of UniProt Q54G86
- Every structure of UniProt Q54J69
- Every structure of UniProt Q54VN6
- Every structure of UniProt P14794
- Every structure of UniProt Q551M2
- Every structure of UniProt Q9Y3A5
- Every structure of UniProt P22685
- Every structure of UniProt Q54J50
- Elsewhere: RCSB PDB 6QKL · PDBe 6QKL · UniProt P34113 · UniProt Q54XI5 · UniProt Q54G86 · UniProt Q54J69 · UniProt Q54VN6 · UniProt P14794 · UniProt Q551M2 · UniProt Q9Y3A5 · UniProt P22685 · UniProt Q54J50
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