MolNFT v2 · #10897 · protein + RNA
Structure of the Thermus thermophilus 30S Ribosomal Subunit
1J5E · 16S ribosomal RNA: “Structure of the Thermus thermophilus 30S Ribosomal Subunit”. X-ray diffraction at 3.05, 2 ligands (ZN, UNX), 20 pockets (best druggability 0.89). MolNFT v2 #10897 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1J5E
- Type
- protein + RNA
- Length
- 3,909 residues
- Chains
- 21
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.05
- Source
- Thermus thermophilus
- Molecule
- 16S ribosomal RNA; 30S ribosomal protein S2; 30S ribosomal protein S3; 30S ribosomal…
- UniProt
- P80373, P27152, P23370, P17291, P24319, P80375, P17293, P24320, P80378, P80379, P24321, P80381, P32193
- Ligands
- ZN, UNX
- Pockets
- 20 · best druggability 0.89
Structure
x-ray diffraction · resolution 3.05 · 21 distinct chains · 35% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S ribosomal RNA | rna | 1513 | — | — |
| B | 30S ribosomal protein S2 | protein | 234 | 47% helix, 11% strand | — |
| C | 30S ribosomal protein S3 | protein | 206 | 34% helix, 17% strand | — |
| D | 30S ribosomal protein S4 | protein | 208 | 40% helix, 6% strand | P80373 |
| E | 30S ribosomal protein S5 | protein | 150 | 29% helix, 37% strand | P27152 |
| F | 30S ribosomal protein S6 | protein | 101 | 31% helix, 45% strand | P23370 |
| G | 30S ribosomal protein S7 | protein | 155 | 55% helix, 6% strand | P17291 |
| H | 30S ribosomal protein S8 | protein | 138 | 26% helix, 30% strand | P24319 |
| I | 30S ribosomal protein S9 | protein | 127 | 30% helix, 16% strand | — |
| J | 30S ribosomal protein S10 | protein | 98 | 13% helix, 26% strand | P80375 |
| K | 30S ribosomal protein S11 | protein | 119 | 25% helix, 27% strand | — |
| L | 30S ribosomal protein S12 | protein | 124 | 5% helix, 23% strand | P17293 |
| M | 30S ribosomal protein S13 | protein | 125 | 46% helix, 2% strand | — |
| N | 30S ribosomal protein S14 | protein | 60 | 37% helix, 7% strand | P24320 |
| O | 30S ribosomal protein S15 | protein | 88 | 73% helix, 0% strand | P80378 |
| P | 30S ribosomal protein S16 | protein | 83 | 20% helix, 20% strand | P80379 |
| Q | 30S ribosomal protein S17 | protein | 104 | 13% helix, 42% strand | P24321 |
| R | 30S ribosomal protein S18 | protein | 73 | 37% helix, 8% strand | — |
| S | 30S ribosomal protein S19 | protein | 80 | 23% helix, 14% strand | P80381 |
| T | 30S ribosomal protein S20 | protein | 99 | 68% helix, 0% strand | — |
| V | 30S ribosomal protein thx | protein | 24 | 25% helix, 0% strand | P32193 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains D, N
- UNX · Unknown atom or ion · ion · 188 copies · chains A, N, E, D, T, L, V, B, M
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 | 1076 | 0.89 | 0.91 | 92 | UNX |
| 2 | 909 | 0.86 | 0.89 | 89 | UNX |
| 3 | 893 | 0.85 | 0.87 | 84 | UNX |
| 4 | 1032 | 0.84 | 0.85 | 80 | UNX |
| 5 | 833 | 0.84 | 0.87 | 71 | UNX |
Interfaces
43 interfaces between chains.
- A–L · 3198 Ų buried · 87 hydrogen bonds · protein-nucleic
- A–I · 2993 Ų buried · 101 hydrogen bonds · protein-nucleic
- A–D · 2952 Ų buried · 92 hydrogen bonds · protein-nucleic
- A–Q · 2753 Ų buried · 78 hydrogen bonds · protein-nucleic
- A–T · 2618 Ų buried · 67 hydrogen bonds · protein-nucleic
Compared structures
- 1J5E · Structure of the thermus thermophilus 30S ribosomal subunit · 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 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 1J5E · PDBe 1J5E · 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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