Research workbench
Structure of the thermus thermophilus 30S ribosomal subunit bound to codon and near-cognate transfer RNA anticodon stem-loop mismatched at the second codon position at the a site with paromomycin
Analyse Structure of the thermus thermophilus 30S ribosomal subunit bound to codon and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1N33
- Type
- protein + RNA
- Length
- 3,917 residues
- Chains
- 23
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S ribosomal RNA; Anticodon stem-loop of ser transfer RNA; A-site messenger RNA…
- UniProt
- P80373, P27152, P23370, P17291, P24319, P80375, P17293, P24320, P80378, P80379, P24321, P80381, P32193
- Ligands
- PAR, MG, ZN
- Pockets
- 20 · best druggability 0.88
Structure
x-ray diffraction · 23 distinct chains · 33% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1513 | — | — |
| Y | Anticodon stem-loop of ser transfer RNA | rna | 11 | — | — |
| Z | A-site messenger RNA fragment | rna | 4 | — | — |
| B | 30S ribosomal protein S2 | protein | 234 | 44% helix, 8% strand | — |
| C | 30S ribosomal protein S3 | protein | 206 | 29% helix, 11% strand | — |
| D | 30S ribosomal protein S4 | protein | 208 | 40% helix, 8% strand | P80373 |
| E | 30S ribosomal protein S5 | protein | 150 | 29% helix, 34% strand | P27152 |
| F | 30S ribosomal protein S6 | protein | 101 | 25% helix, 32% strand | P23370 |
| G | 30S ribosomal protein S7 | protein | 155 | 53% helix, 5% strand | P17291 |
| H | 30S ribosomal protein S8 | protein | 138 | 30% helix, 26% strand | P24319 |
| I | 30S ribosomal protein S9 | protein | 127 | 31% helix, 15% strand | — |
| J | 30S ribosomal protein S10 | protein | 98 | 12% helix, 21% strand | P80375 |
| K | 30S ribosomal protein S11 | protein | 119 | 24% helix, 23% strand | — |
| L | 30S ribosomal protein S12 | protein | 124 | 6% helix, 20% strand | P17293 |
| M | 30S ribosomal protein S13 | protein | 118 | 43% helix, 0% strand | — |
| N | 30S ribosomal protein S14 | protein | 60 | 22% helix, 5% strand | P24320 |
| O | 30S ribosomal protein S15 | protein | 88 | 72% helix, 0% strand | P80378 |
| P | 30S ribosomal protein S16 | protein | 83 | 20% helix, 29% strand | P80379 |
| Q | 30S ribosomal protein S17 | protein | 104 | 11% helix, 47% strand | P24321 |
| R | 30S ribosomal protein S18 | protein | 73 | 37% helix, 5% strand | — |
| S | 30S ribosomal protein S19 | protein | 80 | 24% helix, 13% strand | P80381 |
| T | 30S ribosomal protein S20 | protein | 99 | 71% helix, 2% strand | — |
| V | 30S ribosomal protein thx | protein | 24 | 29% helix, 0% strand | P32193 |
Ligands and binding sites
- PAR · Paromomycin · ligand · chains A
- MG · Magnesium ion · metal · 106 copies · chains A, D, N, V, L, T, Z, J, P, Y
- 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 | 1095 | 0.88 | 0.90 | 81 | MG |
| 2 | 882 | 0.85 | 0.88 | 87 | empty |
| 3 | 934 | 0.85 | 0.87 | 88 | MG |
| 4 | 1054 | 0.85 | 0.86 | 77 | MG |
| 5 | 634 | 0.84 | 0.90 | 67 | MG |
Interfaces
46 interfaces between chains.
- A–L · 3357 Ų buried · 89 hydrogen bonds · protein-nucleic
- A–D · 3020 Ų buried · 90 hydrogen bonds · protein-nucleic
- A–I · 2954 Ų buried · 89 hydrogen bonds · protein-nucleic
- A–Q · 2764 Ų buried · 57 hydrogen bonds · protein-nucleic
- A–T · 2669 Ų buried · 65 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 1 modified (nucleotide modification).
Compared structures
- 1N33 · Structure of the Thermus thermophilus 30S ribosomal subunit bound to codon and… · the same entry in another collection · chain I against I, 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 P80379
- Every structure of UniProt P24321
- Every structure of UniProt P80381
- Every structure of UniProt P32193
- Elsewhere: RCSB PDB 1N33 · PDBe 1N33 · UniProt P80373 · UniProt P27152 · UniProt P23370 · UniProt P17291 · UniProt P24319 · UniProt P80375 · UniProt P17293 · UniProt P24320 · UniProt P80378 · UniProt P80379 · UniProt P24321 · UniProt P80381 · UniProt P32193
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