Research workbench
Structure of the thermus thermophilus 30S ribosomal subunit complexed with a human anti-codon stem loop (hasl) of transfer RNA lysine 3 (TRNALYS3) bound to an mRNA with an aag-codon in the a-site and paromomycin
Analyse Structure of the thermus thermophilus 30S ribosomal subunit complexed with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3T1Y
- Type
- protein + RNA
- Length
- 3,923 residues
- Chains
- 23
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal protein S4…
- UniProt
- P80371, P80372, P80373, Q5SHQ5, Q5SLP8, P17291, Q5SHQ2, P62669, Q5SHN7, P80376, Q5SHN3, P80377, Q5SHQ1, Q5SJ76, Q5SJH3, P24321, P80382, Q5SHP2, P62661, Q5SIH3
- Ligands
- PAR, MG, ZN
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 23 distinct chains · 34% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA | rna | 1513 | — | — |
| B | 30S ribosomal protein S2 | protein | 234 | 41% helix, 10% strand | P80371 |
| C | 30S ribosomal protein S3 | protein | 206 | 32% helix, 21% strand | P80372 |
| D | 30S ribosomal protein S4 | protein | 208 | 38% helix, 8% strand | P80373 |
| E | 30S ribosomal protein S5 | protein | 150 | 30% helix, 37% strand | Q5SHQ5 |
| F | 30S ribosomal protein S6 | protein | 101 | 30% helix, 40% strand | Q5SLP8 |
| G | 30S ribosomal protein S7 | protein | 155 | 53% helix, 6% strand | P17291 |
| H | 30S ribosomal protein S8 | protein | 138 | 30% helix, 35% strand | Q5SHQ2 |
| I | 30S ribosomal protein S9 | protein | 127 | 24% helix, 19% strand | P62669 |
| J | 30S ribosomal protein S10 | protein | 98 | 13% helix, 21% strand | Q5SHN7 |
| K | 30S ribosomal protein S11 | protein | 119 | 26% helix, 29% strand | P80376 |
| L | 30S ribosomal protein S12 | protein | 124 | 6% helix, 23% strand | Q5SHN3 |
| M | 30S ribosomal protein S13 | protein | 125 | 47% helix, 2% strand | P80377 |
| N | 30S ribosomal protein S14 type Z | protein | 60 | 25% helix, 7% strand | Q5SHQ1 |
| O | 30S ribosomal protein S15 | protein | 88 | 72% helix, 0% strand | Q5SJ76 |
| P | 30S ribosomal protein S16 | protein | 83 | 20% helix, 27% strand | Q5SJH3 |
| Q | 30S ribosomal protein S17 | protein | 104 | 14% helix, 42% strand | P24321 |
| R | 30S ribosomal protein S18 | protein | 73 | 42% helix, 8% strand | P80382 |
| S | 30S ribosomal protein S19 | protein | 80 | 18% helix, 16% strand | Q5SHP2 |
| T | 30S ribosomal protein S20 | protein | 99 | 70% helix, 0% strand | P62661 |
| V | 30S ribosomal protein thx | protein | 24 | 29% helix, 8% strand | Q5SIH3 |
| W | MRNA a-site fragment | rna | 3 | — | — |
| X | TRNA asl human LYS3 | rna | 11 | — | — |
Ligands and binding sites
- PAR · Paromomycin · ligand · chains A
- MG · Magnesium ion · metal · 186 copies · chains A, I, N, T, E, S, M, C, L, V, B
- 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 | 704 | 0.85 | 0.90 | 54 | empty |
| 2 | 1057 | 0.85 | 0.87 | 88 | MG |
| 3 | 910 | 0.84 | 0.87 | 83 | MG |
| 4 | 657 | 0.83 | 0.88 | 70 | MG |
| 5 | 410 | 0.82 | 0.92 | 35 | MG |
Interfaces
46 interfaces between chains.
- A–L · 3261 Ų buried · 92 hydrogen bonds · protein-nucleic
- A–I · 3056 Ų buried · 98 hydrogen bonds · protein-nucleic
- A–D · 2980 Ų buried · 98 hydrogen bonds · protein-nucleic
- A–Q · 2663 Ų buried · 62 hydrogen bonds · protein-nucleic
- A–T · 2620 Ų buried · 72 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 3T1Y · Structure of the Thermus thermophilus 30S ribosomal subunit complexed with a human… · 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 P80371
- Every structure of UniProt P80372
- 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 P62669
- 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 Q5SJH3
- Every structure of UniProt P24321
- Every structure of UniProt P80382
- Every structure of UniProt Q5SHP2
- Every structure of UniProt P62661
- Every structure of UniProt Q5SIH3
- Elsewhere: RCSB PDB 3T1Y · PDBe 3T1Y · UniProt P80371 · UniProt P80372 · UniProt P80373 · UniProt Q5SHQ5 · UniProt Q5SLP8 · UniProt P17291 · UniProt Q5SHQ2 · UniProt P62669 · UniProt Q5SHN7 · UniProt P80376 · UniProt Q5SHN3 · UniProt P80377 · UniProt Q5SHQ1 · UniProt Q5SJ76 · UniProt Q5SJH3 · UniProt P24321 · UniProt P80382 · UniProt Q5SHP2 · UniProt P62661 · UniProt Q5SIH3
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