Research workbench
30S ribosomal subunit with rsga bound in the presence of gmppnp
Analyse 30S ribosomal subunit with rsga bound in the presence of gmppnp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2YKR
- Type
- protein + RNA
- Length
- 4,165 residues
- Chains
- 22
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal protein S4…
- EC
- 3.6.1.-
- UniProt
- B7NID0, A1AGK2, A1AGI7, D6JG86, B6I2A6, E3XT25, B6I220, Q0TCN6, A7ZSL0, B7M103, P0A7S4, A1AGI9, B7M1M1, B3HGB0, B7N6J5, P0AG65, E3PE70, B6I230, B7L4E5, B1LF57, E3PE32
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 22 distinct chains · 28% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA | rna | 1533 | — | — |
| B | 30S ribosomal protein S2 | protein | 218 | 22% helix, 11% strand | B7NID0 |
| C | 30S ribosomal protein S3 | protein | 206 | 32% helix, 25% strand | A1AGK2 |
| D | 30S ribosomal protein S4 | protein | 205 | 37% helix, 4% strand | A1AGI7 |
| E | 30S ribosomal protein S5 | protein | 150 | 19% helix, 23% strand | D6JG86 |
| F | 30S ribosomal protein S6 | protein | 100 | 25% helix, 29% strand | B6I2A6 |
| G | 30S ribosomal protein S7 | protein | 151 | 47% helix, 1% strand | E3XT25 |
| H | 30S ribosomal protein S8 | protein | 129 | 24% helix, 20% strand | B6I220 |
| I | 30S ribosomal protein S9 | protein | 127 | 17% helix, 12% strand | Q0TCN6 |
| J | 30S ribosomal protein S10 | protein | 98 | 23% helix, 30% strand | A7ZSL0 |
| K | 30S ribosomal protein S11 | protein | 117 | 19% helix, 26% strand | B7M103 |
| L | 30S ribosomal protein S12 | protein | 123 | 5% helix, 19% strand | P0A7S4 |
| M | 30S ribosomal protein S13 | protein | 114 | 34% helix, 0% strand | A1AGI9 |
| N | 30S ribosomal protein S14 | protein | 96 | 21% helix, 5% strand | B7M1M1 |
| O | 30S ribosomal protein S15 | protein | 88 | 70% helix, 0% strand | B3HGB0 |
| P | 30S ribosomal protein S16 | protein | 82 | 17% helix, 24% strand | B7N6J5 |
| Q | 30S ribosomal protein S17 | protein | 80 | 0% helix, 51% strand | P0AG65 |
| R | 30S ribosomal protein S18 | protein | 55 | 36% helix, 0% strand | E3PE70 |
| S | 30S ribosomal protein S19 | protein | 79 | 20% helix, 15% strand | B6I230 |
| T | 30S ribosomal protein S20 | protein | 85 | 76% helix, 0% strand | B7L4E5 |
| U | 30S ribosomal protein S21 | protein | 51 | 8% helix, 0% strand | B1LF57 |
| W | Putative ribosome biogenesis GTPase rsga (EC 3.6.1.-) | protein | 278 | 32% helix, 20% strand | E3PE32 |
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 | 747 | 0.82 | 0.86 | 57 | empty |
| 2 | 1058 | 0.81 | 0.83 | 72 | empty |
| 3 | 974 | 0.80 | 0.83 | 62 | empty |
| 4 | 863 | 0.79 | 0.83 | 67 | empty |
| 5 | 1079 | 0.79 | 0.82 | 88 | empty |
Interfaces
44 interfaces between chains.
- A–D · 3906 Ų buried · 266 hydrogen bonds · protein-nucleic
- A–L · 3671 Ų buried · 244 hydrogen bonds · protein-nucleic
- A–I · 3087 Ų buried · 226 hydrogen bonds · protein-nucleic
- A–N · 2768 Ų buried · 197 hydrogen bonds · protein-nucleic
- A–G · 2395 Ų buried · 177 hydrogen bonds · protein-nucleic
Compared structures
- 2YKR · 30S ribosomal subunit with RsgA bound in the presence of GMPPNP · the same entry in another collection · chain K against K, 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 B7NID0
- Every structure of UniProt A1AGK2
- Every structure of UniProt A1AGI7
- Every structure of UniProt D6JG86
- Every structure of UniProt B6I2A6
- Every structure of UniProt E3XT25
- Every structure of UniProt B6I220
- Every structure of UniProt Q0TCN6
- Every structure of UniProt A7ZSL0
- Every structure of UniProt B7M103
- Every structure of UniProt P0A7S4
- Every structure of UniProt A1AGI9
- Every structure of UniProt B7M1M1
- Every structure of UniProt B3HGB0
- Every structure of UniProt B7N6J5
- Every structure of UniProt P0AG65
- Every structure of UniProt E3PE70
- Every structure of UniProt B6I230
- Every structure of UniProt B7L4E5
- Every structure of UniProt B1LF57
- Every structure of UniProt E3PE32
- Elsewhere: RCSB PDB 2YKR · PDBe 2YKR · UniProt B7NID0 · UniProt A1AGK2 · UniProt A1AGI7 · UniProt D6JG86 · UniProt B6I2A6 · UniProt E3XT25 · UniProt B6I220 · UniProt Q0TCN6 · UniProt A7ZSL0 · UniProt B7M103 · UniProt P0A7S4 · UniProt A1AGI9 · UniProt B7M1M1 · UniProt B3HGB0 · UniProt B7N6J5 · UniProt P0AG65 · UniProt E3PE70 · UniProt B6I230 · UniProt B7L4E5 · UniProt B1LF57 · UniProt E3PE32
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