Research workbench
The path of messenger RNA through the ribosome. this file, 1JGP, contains the 30S ribosome subunit, three tRNA, and mRNA molecules. 50S ribosome subunit is in the file 1GIY
Analyse The path of messenger RNA through the ribosome. this file, 1JGP, contains the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1JGP
- Type
- protein + RNA
- Length
- 2,628 residues
- Chains
- 24
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- TRNA(PHE); Messenger RNA MV36; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S…
- UniProt
- P80371, P80373, Q5SHQ5, Q5SLP8, P17291, Q5SHQ2, P80374, Q5SHN7, P80376, Q5SHN3, P80377, Q5SHQ1, Q5SJ76, P80381, P32193
- Pockets
- 12 · best druggability 0.67
Structure
x-ray diffraction · 23 distinct chains · 0% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, C | TRNA(PHE) | rna | 76 | — | — |
| D | TRNA(PHE) | rna | 74 | — | — |
| 1 | Messenger RNA MV36 | rna | 6 | — | — |
| E | 30S ribosomal protein S2 | protein | 234 | 0% helix, 0% strand | P80371 |
| F | 30S ribosomal protein S3 | protein | 206 | 0% helix, 0% strand | — |
| G | 30S ribosomal protein S4 | protein | 208 | 0% helix, 0% strand | P80373 |
| H | 30S ribosomal protein S5 | protein | 150 | 0% helix, 0% strand | Q5SHQ5 |
| I | 30S ribosomal protein S6 | protein | 101 | 0% helix, 0% strand | Q5SLP8 |
| J | 30S ribosomal protein S7 | protein | 155 | 0% helix, 0% strand | P17291 |
| K | 30S ribosomal protein S8 | protein | 138 | 0% helix, 0% strand | Q5SHQ2 |
| L | 30S ribosomal protein S9 | protein | 127 | 0% helix, 0% strand | P80374 |
| M | 30S ribosomal protein S10 | protein | 98 | 0% helix, 0% strand | Q5SHN7 |
| N | 30S ribosomal protein S11 | protein | 119 | 0% helix, 0% strand | P80376 |
| O | 30S ribosomal protein S12 | protein | 124 | 0% helix, 0% strand | Q5SHN3 |
| P | 30S ribosomal protein S13 | protein | 125 | 0% helix, 0% strand | P80377 |
| Q | 30S ribosomal protein S14 | protein | 60 | 0% helix, 0% strand | Q5SHQ1 |
| R | 30S ribosomal protein S15 | protein | 88 | 0% helix, 0% strand | Q5SJ76 |
| S | 30S ribosomal protein S16 | protein | 83 | 0% helix, 0% strand | — |
| T | 30S ribosomal protein S17 | protein | 104 | 0% helix, 0% strand | — |
| U | 30S ribosomal protein S18 | protein | 73 | 0% helix, 0% strand | — |
| V | 30S ribosomal protein S19 | protein | 80 | 0% helix, 0% strand | P80381 |
| W | 30S ribosomal protein S20 | protein | 99 | 0% helix, 0% strand | — |
| X | 30S ribosomal protein thx | protein | 24 | 0% helix, 0% strand | P32193 |
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 727 | 0.67 | 0.76 | 31 | empty |
| 2 | 842 | 0.67 | 0.75 | 40 | empty |
| 3 | 620 | 0.61 | 0.74 | 33 | empty |
| 4 | 348 | 0.59 | 0.78 | 25 | empty |
| 5 | 440 | 0.59 | 0.76 | 28 | empty |
Interfaces
18 interfaces between chains.
- D–J · 289 Ų buried · 0 hydrogen bonds · protein-nucleic
- I–U · 176 Ų buried · 0 hydrogen bonds · protein-protein
- M–Q · 160 Ų buried · 0 hydrogen bonds · protein-protein
- C–1 · 158 Ų buried · 8 hydrogen bonds · nucleic-nucleic
- B–1 · 154 Ų buried · 9 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 34 modified (nucleotide modification).
Compared structures
- 1JGP · The Path of Messenger RNA Through the Ribosome. THIS FILE, 1JGP, CONTAINS THE 30S… · the same entry in another collection · chain B against B, 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 P80371
- Every structure of UniProt P80373
- Every structure of UniProt Q5SHQ5
- Every structure of UniProt Q5SLP8
- Every structure of UniProt P17291
- Every structure of UniProt Q5SHQ2
- Every structure of UniProt P80374
- Every structure of UniProt Q5SHN7
- Every structure of UniProt P80376
- Every structure of UniProt Q5SHN3
- Every structure of UniProt P80377
- Every structure of UniProt Q5SHQ1
- Every structure of UniProt Q5SJ76
- Every structure of UniProt P80381
- Every structure of UniProt P32193
- Elsewhere: RCSB PDB 1JGP · PDBe 1JGP · UniProt P80371 · UniProt P80373 · UniProt Q5SHQ5 · UniProt Q5SLP8 · UniProt P17291 · UniProt Q5SHQ2 · UniProt P80374 · UniProt Q5SHN7 · UniProt P80376 · UniProt Q5SHN3 · UniProt P80377 · UniProt Q5SHQ1 · UniProt Q5SJ76 · UniProt P80381 · UniProt P32193
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