MolNFT v1 · #113704 · protein + RNA
Mechanism of EIF6 release from the nascent 60S ribosomal subunit
5ANC · 60S ribosomal protein L3: “Mechanism of EIF6 release from the nascent 60S ribosomal subunit”. Electron microscopy, 20 pockets (best druggability 0.85). MolNFT v1 #113704 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ANC
- Type
- protein + RNA
- Length
- 3,963 residues
- Chains
- 11
- 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, Q9Y3A5, Q7Z2Z2
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 11 distinct chains · 21% helix, 14% 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, 32% strand | Q54XI5 |
| C | 60S acidic ribosomal protein P0 | protein | 205 | 15% helix, 9% strand | P22685 |
| D | 60S ribosomal protein L12 | protein | 166 | 17% helix, 6% strand | Q54J50 |
| E | 60S ribosomal protein L23 | protein | 136 | 8% helix, 26% strand | Q54G86 |
| F | 60S ribosomal protein L10 | protein | 217 | 17% helix, 18% strand | Q54J69 |
| G | 60S ribosomal protein L24 | protein | 69 | 22% helix, 12% strand | Q54VN6 |
| H | Ubiquitin-60S ribosomal protein L40 | protein | 52 | 21% helix, 4% strand | P14794 |
| J | Ribosome maturation protein sbds | protein | 250 | 35% helix, 13% strand | Q9Y3A5 |
| K | Elongation factor tu GTP-binding domain-containing protein 1 | protein | 1120 | 26% helix, 9% 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 | 1096 | 0.85 | 0.86 | 74 | empty |
| 2 | 874 | 0.84 | 0.87 | 80 | empty |
| 3 | 1105 | 0.84 | 0.85 | 90 | empty |
| 4 | 128 | 0.81 | 0.98 | 30 | empty |
| 5 | 610 | 0.80 | 0.86 | 59 | empty |
Interfaces
23 interfaces between chains.
- A–N · 6308 Ų buried · 123 hydrogen bonds · protein-nucleic
- F–N · 3628 Ų buried · 73 hydrogen bonds · protein-nucleic
- J–N · 2545 Ų buried · 53 hydrogen bonds · protein-nucleic
- C–N · 2240 Ų buried · 58 hydrogen bonds · protein-nucleic
- B–N · 2162 Ų buried · 28 hydrogen bonds · protein-nucleic
Compared structures
- 5ANC · Mechanism of eIF6 release from the nascent 60S ribosomal subunit · the same entry in another collection · chain N against N, TM-score 1.00
- 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 0.93
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 Q9Y3A5
- Every structure of UniProt Q7Z2Z2
- Elsewhere: RCSB PDB 5ANC · PDBe 5ANC · UniProt P34113 · UniProt Q54XI5 · UniProt P22685 · UniProt Q54J50 · UniProt Q54G86 · UniProt Q54J69 · UniProt Q54VN6 · UniProt P14794 · UniProt Q9Y3A5 · UniProt Q7Z2Z2
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