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
- 5ANB
- Type
- protein + RNA
- Length
- 4,187 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 60S ribosomal protein L3; 60S ribosomal protein L9; 60S acidic ribosomal protein P0; 60S…
- UniProt
- P34113, Q54XI5, P22685, Q54J50, Q54G86, Q54J69, Q54VN6, P14794, Q551M2, Q9Y3A5, Q7Z2Z2
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 12 distinct chains · 23% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 60S ribosomal protein L3 | protein | 398 | 13% helix, 19% strand | P34113 |
| B | 60S ribosomal protein L9 | protein | 188 | 19% helix, 36% strand | Q54XI5 |
| C | 60S acidic ribosomal protein P0 | protein | 205 | 13% helix, 10% strand | P22685 |
| D | 60S ribosomal protein L12 | protein | 166 | 17% helix, 2% strand | Q54J50 |
| E | 60S ribosomal protein L23 | protein | 136 | 8% helix, 31% strand | Q54G86 |
| F | 60S ribosomal protein L10 | protein | 217 | 17% helix, 22% strand | Q54J69 |
| G | 60S ribosomal protein L24 | protein | 69 | 29% helix, 17% strand | Q54VN6 |
| H | Ubiquitin-60S ribosomal protein L40 | protein | 52 | 19% helix, 13% strand | P14794 |
| I | Eukaryotic translation initiation factor 6 | protein | 224 | 25% helix, 22% strand | Q551M2 |
| J | Ribosome maturation protein sbds | protein | 250 | 39% helix, 18% strand | Q9Y3A5 |
| K | Elongation factor tu GTP-binding domain-containing protein 1 | protein | 1120 | 29% helix, 10% strand | Q7Z2Z2 |
| N | 26S ribosomal RNA | rna | 1162 | — | — |
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 | 1092 | 0.84 | 0.86 | 63 | empty |
| 2 | 860 | 0.84 | 0.87 | 75 | empty |
| 3 | 598 | 0.82 | 0.89 | 50 | empty |
| 4 | 522 | 0.81 | 0.88 | 62 | empty |
| 5 | 190 | 0.81 | 0.96 | 27 | empty |
Interfaces
24 interfaces between chains.
- A–N · 6185 Ų buried · 121 hydrogen bonds · protein-nucleic
- F–N · 3676 Ų buried · 70 hydrogen bonds · protein-nucleic
- J–N · 2566 Ų buried · 46 hydrogen bonds · protein-nucleic
- E–N · 2205 Ų buried · 36 hydrogen bonds · protein-nucleic
- B–N · 2080 Ų buried · 30 hydrogen bonds · protein-nucleic
Compared structures
- Q551M2 · AlphaFold monomer V2.0 prediction for eukaryotic translation initiation factor 6 (Q551M2) · a predicted model of the same protein · chain I against A, TM-score 0.95
- Q54XI5 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L9 (Q54XI5) · a predicted model of the same protein · chain B against A, TM-score 0.94
- Q54G86 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L23 (Q54G86) · a predicted model of the same protein · chain E against A, TM-score 0.94
- Q54J69 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L10 (Q54J69) · a predicted model of the same protein · chain F against A, TM-score 0.93
- 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 0.91
- P14794 · AlphaFold monomer V2.0 prediction for ubiquitin-60S ribosomal protein L40 (P14794) · a predicted model of the same protein · chain H against A, TM-score 0.87
- Q7Z2Z2 · AlphaFold monomer V2.0 prediction for elongation factor-like GTPase 1 (Q7Z2Z2) · a predicted model of the same protein · chain K against A, TM-score 0.74
- P22685 · AlphaFold monomer V2.0 prediction for 60S acidic ribosomal protein P0 (P22685) · a predicted model of the same protein · chain C against A, TM-score 0.69
- Q54J50 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L12 (Q54J50) · a predicted model of the same protein · chain D against A, TM-score 0.67
- Q54VN6 · AlphaFold monomer V2.0 prediction for 60S ribosomal protein L24 (Q54VN6) · a predicted model of the same protein · chain G against A, TM-score 0.67
- Q9Y3A5 · AlphaFold monomer V2.0 prediction for ribosome maturation protein sbds (Q9Y3A5) · a predicted model of the same protein · chain J against A, TM-score 0.63
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 P22685
- Every structure of UniProt Q54J50
- 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 Q7Z2Z2
- Elsewhere: RCSB PDB 5ANB · PDBe 5ANB · UniProt P34113 · UniProt Q54XI5 · UniProt P22685 · UniProt Q54J50 · UniProt Q54G86 · UniProt Q54J69 · UniProt Q54VN6 · UniProt P14794 · UniProt Q551M2 · UniProt Q9Y3A5 · UniProt Q7Z2Z2
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