Research workbench
Structure of the thermus thermophilus 30S ribosomal subunit in complex with the antibiotic paromomycin
Analyse Structure of the thermus thermophilus 30S ribosomal subunit in complex with the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1IBK
- Type
- protein + RNA
- Length
- 3,908 residues
- Chains
- 22
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; P-site messenger RNA fragment; 30S ribosomal protein S2; 30S ribosomal…
- UniProt
- P80373, P27152, P23370, P17291, P24319, P80375, P17293, P24320, P80378, P80381, P32193
- Ligands
- PAR, MG, ZN
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · 22 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1506 | — | — |
| X | P-site messenger RNA fragment | rna | 6 | — | — |
| B | 30S ribosomal protein S2 | protein | 234 | 47% helix, 10% strand | — |
| C | 30S ribosomal protein S3 | protein | 206 | 32% helix, 13% strand | — |
| D | 30S ribosomal protein S4 | protein | 208 | 41% helix, 6% strand | P80373 |
| E | 30S ribosomal protein S5 | protein | 150 | 28% helix, 39% strand | P27152 |
| F | 30S ribosomal protein S6 | protein | 101 | 31% helix, 41% strand | P23370 |
| G | 30S ribosomal protein S7 | protein | 155 | 51% helix, 8% strand | P17291 |
| H | 30S ribosomal protein S8 | protein | 138 | 28% helix, 26% strand | P24319 |
| I | 30S ribosomal protein S9 | protein | 127 | 35% helix, 18% strand | — |
| J | 30S ribosomal protein S10 | protein | 98 | 21% helix, 21% strand | P80375 |
| K | 30S ribosomal protein S11 | protein | 119 | 27% helix, 29% strand | — |
| L | 30S ribosomal protein S12 | protein | 124 | 6% helix, 19% strand | P17293 |
| M | 30S ribosomal protein S13 | protein | 125 | 45% helix, 2% strand | — |
| N | 30S ribosomal protein S14 | protein | 60 | 27% helix, 2% strand | P24320 |
| O | 30S ribosomal protein S15 | protein | 88 | 72% helix, 0% strand | P80378 |
| P | 30S ribosomal protein S16 | protein | 83 | 18% helix, 25% strand | — |
| Q | 30S ribosomal protein S17 | protein | 104 | 14% helix, 42% strand | — |
| R | 30S ribosomal protein S18 | protein | 73 | 34% helix, 5% strand | — |
| S | 30S ribosomal protein S19 | protein | 80 | 20% helix, 13% strand | P80381 |
| T | 30S ribosomal protein S20 | protein | 99 | 69% helix, 0% strand | — |
| V | 30S ribosomal protein thx | protein | 24 | 25% helix, 8% strand | P32193 |
Ligands and binding sites
- PAR · Paromomycin · ligand · chains A
- MG · Magnesium ion · metal · 113 copies · chains A, E, N, V, L, D, T, J
- ZN · Zinc ion · metal · 2 copies · chains D, A, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 1084 | 0.89 | 0.92 | 102 | MG |
| 2 | 1112 | 0.86 | 0.88 | 92 | MG |
| 3 | 816 | 0.84 | 0.87 | 70 | MG |
| 4 | 786 | 0.83 | 0.87 | 84 | MG |
| 5 | 489 | 0.82 | 0.89 | 53 | MG |
Interfaces
44 interfaces between chains.
- A–L · 3198 Ų buried · 89 hydrogen bonds · protein-nucleic
- A–I · 2976 Ų buried · 97 hydrogen bonds · protein-nucleic
- A–D · 2963 Ų buried · 83 hydrogen bonds · protein-nucleic
- A–Q · 2750 Ų buried · 72 hydrogen bonds · protein-nucleic
- A–T · 2643 Ų buried · 69 hydrogen bonds · protein-nucleic
Compared structures
- 1IBK · Structure of the thermus thermophilus 30S ribosomal subunit in complex with the… · 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 P80373
- Every structure of UniProt P27152
- Every structure of UniProt P23370
- Every structure of UniProt P17291
- Every structure of UniProt P24319
- Every structure of UniProt P80375
- Every structure of UniProt P17293
- Every structure of UniProt P24320
- Every structure of UniProt P80378
- Every structure of UniProt P80381
- Every structure of UniProt P32193
- Elsewhere: RCSB PDB 1IBK · PDBe 1IBK · UniProt P80373 · UniProt P27152 · UniProt P23370 · UniProt P17291 · UniProt P24319 · UniProt P80375 · UniProt P17293 · UniProt P24320 · UniProt P80378 · UniProt P80381 · UniProt P32193
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