Research workbench
Cryo-EM structure of a late pre-40S ribosomal subunit from saccharomyces cerevisiae
Analyse Cryo-EM structure of a late pre-40S ribosomal subunit from saccharomyces… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6EML
- Type
- protein + RNA
- Length
- 6,908 residues
- Chains
- 32
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pre-18S ribosomal RNA; 40S ribosomal protein S12; 40S ribosomal protein S5; 40S ribosomal…
- EC
- 2.7.11.1
- UniProt
- P48589, P26783, P02407, Q01855, P0CX51, P0CX55, P07280, Q3E792, P0C0X0, P05759, P32905, P33442, P25443, P0CX35, P0CX37, P26786, P0CX39, O13516, P0CX47, P05756, P06367, P0C0V8, P0C0W1, P0CX29, P0CX31, P35997, Q07381, P0CX33, Q99216, P40160, P38333
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 32 distinct chains · 29% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | Pre-18S ribosomal RNA | rna | 1675 | — | — |
| D | 40S ribosomal protein S12 | protein | 124 | 23% helix, 2% strand | P48589 |
| B | 40S ribosomal protein S5 | protein | 202 | 46% helix, 2% strand | P26783 |
| C | 40S ribosomal protein S17-a | protein | 114 | 38% helix, 4% strand | P02407 |
| E | 40S ribosomal protein S15 | protein | 117 | 19% helix, 13% strand | Q01855 |
| F | 40S ribosomal protein S16-a | protein | 141 | 28% helix, 19% strand | P0CX51 |
| H | 40S ribosomal protein S18-a | protein | 122 | 39% helix, 8% strand | P0CX55 |
| I | 40S ribosomal protein S19-a | protein | 143 | 45% helix, 8% strand | P07280 |
| K | 40S ribosomal protein S25-a | protein | 64 | 28% helix, 11% strand | Q3E792 |
| L | 40S ribosomal protein S28-B | protein | 62 | 0% helix, 26% strand | P0C0X0 |
| N | Ubiquitin-40S ribosomal protein S31 | protein | 51 | 0% helix, 0% strand | P05759 |
| P | 40S ribosomal protein S0-a | protein | 206 | 28% helix, 8% strand | P32905 |
| Q | 40S ribosomal protein S1-a | protein | 214 | 24% helix, 29% strand | P33442 |
| R | 40S ribosomal protein S2 | protein | 220 | 28% helix, 20% strand | P25443 |
| S | 40S ribosomal protein S4-a | protein | 260 | 14% helix, 27% strand | P0CX35 |
| T | 40S ribosomal protein S6-a | protein | 226 | 24% helix, 23% strand | P0CX37 |
| U | 40S ribosomal protein S7-a | protein | 184 | 28% helix, 19% strand | P26786 |
| V | 40S ribosomal protein S8-a | protein | 188 | 23% helix, 21% strand | P0CX39 |
| W | 40S ribosomal protein S9-a | protein | 185 | 42% helix, 3% strand | O13516 |
| X | 40S ribosomal protein S11-a | protein | 155 | 3% helix, 31% strand | P0CX47 |
| Y | 40S ribosomal protein S13 | protein | 150 | 54% helix, 0% strand | P05756 |
| Z | 40S ribosomal protein S14-a | protein | 127 | 27% helix, 12% strand | P06367 |
| a | 40S ribosomal protein S21-a | protein | 87 | 23% helix, 23% strand | P0C0V8 |
| b | 40S ribosomal protein S22-a | protein | 129 | 29% helix, 22% strand | P0C0W1 |
| c | 40S ribosomal protein S23-a | protein | 144 | 17% helix, 22% strand | P0CX29 |
| d | 40S ribosomal protein S24-a | protein | 134 | 34% helix, 26% strand | P0CX31 |
| f | 40S ribosomal protein S27-a | protein | 81 | 6% helix, 20% strand | P35997 |
| t | Ribosome biogenesis protein TSR1 | protein | 633 | 19% helix, 23% strand | Q07381 |
| g | 40S ribosomal protein S30-a | protein | 60 | 25% helix, 0% strand | P0CX33 |
| p | Pre-rRNA-processing protein PNO1 | protein | 185 | 45% helix, 14% strand | Q99216 |
| r | SERINE/THREONINE-protein kinase RIO2 (EC 2.7.11.1) | protein | 264 | 38% helix, 15% strand | P40160 |
| e | Essential nuclear protein 1 | protein | 261 | 60% helix, 0% strand | P38333 |
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 | 1082 | 0.88 | 0.90 | 83 | empty |
| 2 | 938 | 0.87 | 0.90 | 77 | empty |
| 3 | 1176 | 0.86 | 0.88 | 92 | empty |
| 4 | 795 | 0.86 | 0.89 | 84 | empty |
| 5 | 472 | 0.86 | 0.93 | 56 | empty |
Interfaces
82 interfaces between chains.
- 2–T · 5219 Ų buried · 120 hydrogen bonds · protein-nucleic
- 2–S · 4003 Ų buried · 69 hydrogen bonds · protein-nucleic
- 2–V · 3894 Ų buried · 110 hydrogen bonds · protein-nucleic
- 2–W · 3861 Ų buried · 84 hydrogen bonds · protein-nucleic
- 2–c · 3494 Ų buried · 62 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 isopeptide (isopeptide).
Compared structures
- 6EML · Cryo-EM structure of a late pre-40S ribosomal subunit from Saccharomyces cerevisiae · the same entry in another collection · chain N against N, TM-score 1.00
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 P48589
- Every structure of UniProt P26783
- Every structure of UniProt P02407
- Every structure of UniProt Q01855
- Every structure of UniProt P0CX51
- Every structure of UniProt P0CX55
- Every structure of UniProt P07280
- Every structure of UniProt Q3E792
- Every structure of UniProt P0C0X0
- Every structure of UniProt P05759
- Every structure of UniProt P32905
- Every structure of UniProt P33442
- Every structure of UniProt P25443
- Every structure of UniProt P0CX35
- Every structure of UniProt P0CX37
- Every structure of UniProt P26786
- Every structure of UniProt P0CX39
- Every structure of UniProt O13516
- Every structure of UniProt P0CX47
- Every structure of UniProt P05756
- Every structure of UniProt P06367
- Every structure of UniProt P0C0V8
- Every structure of UniProt P0C0W1
- Every structure of UniProt P0CX29
- Every structure of UniProt P0CX31
- Every structure of UniProt P35997
- Every structure of UniProt Q07381
- Every structure of UniProt P0CX33
- Every structure of UniProt Q99216
- Every structure of UniProt P40160
- Every structure of UniProt P38333
- Elsewhere: RCSB PDB 6EML · PDBe 6EML · UniProt P48589 · UniProt P26783 · UniProt P02407 · UniProt Q01855 · UniProt P0CX51 · UniProt P0CX55 · UniProt P07280 · UniProt Q3E792 · UniProt P0C0X0 · UniProt P05759 · UniProt P32905 · UniProt P33442 · UniProt P25443 · UniProt P0CX35 · UniProt P0CX37 · UniProt P26786 · UniProt P0CX39 · UniProt O13516 · UniProt P0CX47 · UniProt P05756 · UniProt P06367 · UniProt P0C0V8 · UniProt P0C0W1 · UniProt P0CX29 · UniProt P0CX31 · UniProt P35997 · UniProt Q07381 · UniProt P0CX33 · UniProt Q99216 · UniProt P40160 · UniProt P38333
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