Research workbench
Early cytoplasmic yeast pre-40S particle (purified with TSR1 as bait)
Analyse Early cytoplasmic yeast pre-40S particle (purified with TSR1 as bait) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y7C
- Type
- protein + RNA
- Length
- 7,116 residues
- Chains
- 34
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 20S ribosomal RNA; 40S ribosomal protein S0-a; 40S ribosomal protein S1-a; 40S ribosomal…
- EC
- 2.7.11.1
- UniProt
- P32905, P33442, P25443, P0CX35, P26783, P0CX37, P26786, P0CX39, O13516, P0CX47, P48589, P05756, P06367, Q01855, P0CX51, P02407, P0CX55, P07280, P38701, P0C0V8, P0C0W1, P0CX29, P0CX31, Q3E792, P35997, Q3E7X9, P41057, P0CX33, Q99216, P38333, P34078, P40160, Q07381
- Pockets
- 20 · best druggability 0.90
Structure
electron microscopy · 34 distinct chains · 19% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 2 | 20S ribosomal RNA | rna | 1735 | — | — |
| A | 40S ribosomal protein S0-a | protein | 206 | 29% helix, 14% strand | P32905 |
| B | 40S ribosomal protein S1-a | protein | 214 | 20% helix, 23% strand | P33442 |
| C | 40S ribosomal protein S2 | protein | 220 | 25% helix, 21% strand | P25443 |
| E | 40S ribosomal protein S4-a | protein | 260 | 8% helix, 20% strand | P0CX35 |
| F | 40S ribosomal protein S5 | protein | 206 | 16% helix, 1% strand | P26783 |
| G | 40S ribosomal protein S6-a | protein | 226 | 22% helix, 15% strand | P0CX37 |
| H | 40S ribosomal protein S7-a | protein | 168 | 17% helix, 16% strand | P26786 |
| I | 40S ribosomal protein S8-a | protein | 188 | 20% helix, 24% strand | P0CX39 |
| J | 40S ribosomal protein S9-a | protein | 185 | 36% helix, 1% strand | O13516 |
| L | 40S ribosomal protein S11-a | protein | 155 | 3% helix, 28% strand | P0CX47 |
| M | 40S ribosomal protein S12 | protein | 125 | 19% helix, 5% strand | P48589 |
| N | 40S ribosomal protein S13 | protein | 150 | 43% helix, 0% strand | P05756 |
| O | 40S ribosomal protein S14-a | protein | 128 | 10% helix, 13% strand | P06367 |
| P | 40S ribosomal protein S15 | protein | 127 | 13% helix, 13% strand | Q01855 |
| Q | 40S ribosomal protein S16-a | protein | 127 | 9% helix, 6% strand | P0CX51 |
| R | 40S ribosomal protein S17-a | protein | 115 | 23% helix, 3% strand | P02407 |
| S | 40S ribosomal protein S18-a | protein | 135 | 21% helix, 2% strand | P0CX55 |
| T | 40S ribosomal protein S19-a | protein | 143 | 17% helix, 4% strand | P07280 |
| U | 40S ribosomal protein S20 | protein | 67 | 21% helix, 0% strand | P38701 |
| V | 40S ribosomal protein S21-a | protein | 87 | 15% helix, 24% strand | P0C0V8 |
| W | 40S ribosomal protein S22-a | protein | 129 | 26% helix, 23% strand | P0C0W1 |
| X | 40S ribosomal protein S23-a | protein | 144 | 19% helix, 15% strand | P0CX29 |
| Y | 40S ribosomal protein S24-a | protein | 134 | 24% helix, 21% strand | P0CX31 |
| Z | 40S ribosomal protein S25-a | protein | 63 | 22% helix, 0% strand | Q3E792 |
| b | 40S ribosomal protein S27-a | protein | 81 | 7% helix, 15% strand | P35997 |
| c | 40S ribosomal protein S28-a | protein | 63 | 0% helix, 41% strand | Q3E7X9 |
| d | 40S ribosomal protein S29-a | protein | 27 | 0% helix, 0% strand | P41057 |
| e | 40S ribosomal protein S30-a | protein | 60 | 27% helix, 0% strand | P0CX33 |
| h | Pre-rRNA-processing protein PNO1 | protein | 179 | 26% helix, 12% strand | Q99216 |
| i | Essential nuclear protein 1 | protein | 261 | 15% helix, 1% strand | P38333 |
| j | Protein LTV1 | protein | 55 | 20% helix, 0% strand | P34078 |
| l | SERINE/THREONINE-protein kinase RIO2 (EC 2.7.11.1) | protein | 286 | 28% helix, 10% strand | P40160 |
| t | Ribosome biogenesis protein TSR1 | protein | 667 | 10% helix, 14% strand | Q07381 |
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 | 1046 | 0.90 | 0.91 | 144 | empty |
| 2 | 1102 | 0.88 | 0.90 | 133 | empty |
| 3 | 896 | 0.88 | 0.91 | 93 | empty |
| 4 | 1007 | 0.87 | 0.89 | 94 | empty |
| 5 | 1047 | 0.86 | 0.88 | 78 | empty |
Interfaces
86 interfaces between chains.
- 2–G · 4759 Ų buried · 91 hydrogen bonds · protein-nucleic
- 2–I · 3857 Ų buried · 101 hydrogen bonds · protein-nucleic
- 2–E · 3849 Ų buried · 82 hydrogen bonds · protein-nucleic
- 2–J · 3769 Ų buried · 74 hydrogen bonds · protein-nucleic
- 2–X · 3096 Ų buried · 56 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
Compared structures
- 6Y7C · Early cytoplasmic yeast pre-40S particle (purified with Tsr1 as bait) · the same entry in another collection · chain L against L, 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 P32905
- Every structure of UniProt P33442
- Every structure of UniProt P25443
- Every structure of UniProt P0CX35
- Every structure of UniProt P26783
- 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 P48589
- Every structure of UniProt P05756
- Every structure of UniProt P06367
- Every structure of UniProt Q01855
- Every structure of UniProt P0CX51
- Every structure of UniProt P02407
- Every structure of UniProt P0CX55
- Every structure of UniProt P07280
- Every structure of UniProt P38701
- Every structure of UniProt P0C0V8
- Every structure of UniProt P0C0W1
- Every structure of UniProt P0CX29
- Every structure of UniProt P0CX31
- Every structure of UniProt Q3E792
- Every structure of UniProt P35997
- Every structure of UniProt Q3E7X9
- Every structure of UniProt P41057
- Every structure of UniProt P0CX33
- Every structure of UniProt Q99216
- Every structure of UniProt P38333
- Every structure of UniProt P34078
- Every structure of UniProt P40160
- Every structure of UniProt Q07381
- Elsewhere: RCSB PDB 6Y7C · PDBe 6Y7C · UniProt P32905 · UniProt P33442 · UniProt P25443 · UniProt P0CX35 · UniProt P26783 · UniProt P0CX37 · UniProt P26786 · UniProt P0CX39 · UniProt O13516 · UniProt P0CX47 · UniProt P48589 · UniProt P05756 · UniProt P06367 · UniProt Q01855 · UniProt P0CX51 · UniProt P02407 · UniProt P0CX55 · UniProt P07280 · UniProt P38701 · UniProt P0C0V8 · UniProt P0C0W1 · UniProt P0CX29 · UniProt P0CX31 · UniProt Q3E792 · UniProt P35997 · UniProt Q3E7X9 · UniProt P41057 · UniProt P0CX33 · UniProt Q99216 · UniProt P38333 · UniProt P34078 · UniProt P40160 · UniProt Q07381
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