Research workbench
State 1 of yeast TSR1-tap RPS20-deltaloop pre-40S particles
Analyse State 1 of yeast TSR1-tap RPS20-deltaloop pre-40S particles in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6RBD
- Type
- protein + RNA
- Length
- 7,227 residues
- Chains
- 35
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 40S ribosomal protein S27-a; 40S ribosomal protein S30-a; 20S ribosomal RNA; 40S…
- EC
- 2.7.11.1, 2.1.1.183
- UniProt
- P35997, P0CX33, P32905, P33442, P25443, P0CX35, P0CX37, P26786, P0CX39, O13516, P0CX47, P05756, P0C0V8, P0C0W1, P0CX29, P0CX31, Q3E7X9, P41057, Q99216, P38333, Q07381, P40160, P41819, P26783, P48589, P06367, Q01855, P0CX51, P02407, P0CX55, P07280, Q3E792, P05750, P38701
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 35 distinct chains · 33% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| b | 40S ribosomal protein S27-a | protein | 81 | 7% helix, 36% strand | P35997 |
| e | 40S ribosomal protein S30-a | protein | 48 | 27% helix, 8% strand | P0CX33 |
| 2 | 20S ribosomal RNA | rna | 1777 | — | — |
| A | 40S ribosomal protein S0-a | protein | 206 | 35% helix, 12% strand | P32905 |
| B | 40S ribosomal protein S1-a | protein | 214 | 32% helix, 33% strand | P33442 |
| C | 40S ribosomal protein S2 | protein | 217 | 30% helix, 29% strand | P25443 |
| E | 40S ribosomal protein S4-a | protein | 260 | 13% helix, 32% strand | P0CX35 |
| G | 40S ribosomal protein S6-a | protein | 232 | 27% helix, 26% strand | P0CX37 |
| H | 40S ribosomal protein S7-a | protein | 184 | 34% helix, 22% strand | P26786 |
| I | 40S ribosomal protein S8-a | protein | 188 | 28% helix, 27% strand | P0CX39 |
| J | 40S ribosomal protein S9-a | protein | 185 | 50% helix, 4% strand | O13516 |
| L | 40S ribosomal protein S11-a | protein | 140 | 4% helix, 34% strand | P0CX47 |
| N | 40S ribosomal protein S13 | protein | 150 | 57% helix, 0% strand | P05756 |
| V | 40S ribosomal protein S21-a | protein | 87 | 20% helix, 30% strand | P0C0V8 |
| W | 40S ribosomal protein S22-a | protein | 129 | 31% helix, 26% strand | P0C0W1 |
| X | 40S ribosomal protein S23-a | protein | 144 | 17% helix, 30% strand | P0CX29 |
| Y | 40S ribosomal protein S24-a | protein | 134 | 37% helix, 27% strand | P0CX31 |
| c | 40S ribosomal protein S28-a | protein | 63 | 0% helix, 49% strand | Q3E7X9 |
| d | 40S ribosomal protein S29-a | protein | 37 | 30% helix, 8% strand | P41057 |
| h | Pre-rRNA-processing protein PNO1 | protein | 181 | 55% helix, 19% strand | Q99216 |
| i | Essential nuclear protein 1 | protein | 139 | 68% helix, 0% strand | P38333 |
| k | Ribosome biogenesis protein TSR1 | protein | 605 | 21% helix, 31% strand | Q07381 |
| l | SERINE/THREONINE-protein kinase RIO2 (EC 2.7.11.1) | protein | 271 | 41% helix, 20% strand | P40160 |
| y | Dimethyladenosine transferase (EC 2.1.1.183) | protein | 154 | 37% helix, 13% strand | P41819 |
| F | 40S ribosomal protein S5 | protein | 206 | 48% helix, 4% strand | P26783 |
| M | 40S ribosomal protein S12 | protein | 125 | 42% helix, 19% strand | P48589 |
| O | 40S ribosomal protein S14-a | protein | 127 | 29% helix, 28% strand | P06367 |
| P | 40S ribosomal protein S15 | protein | 114 | 38% helix, 11% strand | Q01855 |
| Q | 40S ribosomal protein S16-a | protein | 127 | 36% helix, 20% strand | P0CX51 |
| R | 40S ribosomal protein S17-a | protein | 125 | 53% helix, 5% strand | P02407 |
| S | 40S ribosomal protein S18-a | protein | 104 | 29% helix, 12% strand | P0CX55 |
| T | 40S ribosomal protein S19-a | protein | 143 | 48% helix, 15% strand | P07280 |
| Z | 40S ribosomal protein S25-a | protein | 63 | 38% helix, 16% strand | Q3E792 |
| D | 40S ribosomal protein S3 | protein | 185 | 36% helix, 29% strand | P05750 |
| U | 40S ribosomal protein S20 | protein | 82 | 33% helix, 43% strand | P38701 |
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 | 885 | 0.87 | 0.89 | 79 | empty |
| 2 | 945 | 0.86 | 0.88 | 94 | empty |
| 3 | 810 | 0.86 | 0.89 | 88 | empty |
| 4 | 1049 | 0.85 | 0.87 | 75 | empty |
| 5 | 767 | 0.85 | 0.88 | 97 | empty |
Interfaces
87 interfaces between chains.
- 2–G · 5272 Ų buried · 115 hydrogen bonds · protein-nucleic
- 2–I · 3843 Ų buried · 122 hydrogen bonds · protein-nucleic
- 2–E · 3800 Ų buried · 61 hydrogen bonds · protein-nucleic
- 2–J · 3384 Ų buried · 64 hydrogen bonds · protein-nucleic
- 2–X · 3350 Ų buried · 65 hydrogen bonds · protein-nucleic
Compared structures
- 6RBD · State 1 of yeast Tsr1-TAP Rps20-Deltaloop pre-40S particles · the same entry in another collection · chain J against J, 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 P35997
- Every structure of UniProt P0CX33
- 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 P0C0V8
- Every structure of UniProt P0C0W1
- Every structure of UniProt P0CX29
- Every structure of UniProt P0CX31
- Every structure of UniProt Q3E7X9
- Every structure of UniProt P41057
- Every structure of UniProt Q99216
- Every structure of UniProt P38333
- Every structure of UniProt Q07381
- Every structure of UniProt P40160
- Every structure of UniProt P41819
- Every structure of UniProt P26783
- Every structure of UniProt P48589
- 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 Q3E792
- Every structure of UniProt P05750
- Every structure of UniProt P38701
- Elsewhere: RCSB PDB 6RBD · PDBe 6RBD · UniProt P35997 · UniProt P0CX33 · UniProt P32905 · UniProt P33442 · UniProt P25443 · UniProt P0CX35 · UniProt P0CX37 · UniProt P26786 · UniProt P0CX39 · UniProt O13516 · UniProt P0CX47 · UniProt P05756 · UniProt P0C0V8 · UniProt P0C0W1 · UniProt P0CX29 · UniProt P0CX31 · UniProt Q3E7X9 · UniProt P41057 · UniProt Q99216 · UniProt P38333 · UniProt Q07381 · UniProt P40160 · UniProt P41819 · UniProt P26783 · UniProt P48589 · UniProt P06367 · UniProt Q01855 · UniProt P0CX51 · UniProt P02407 · UniProt P0CX55 · UniProt P07280 · UniProt Q3E792 · UniProt P05750 · UniProt P38701
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