Research workbench
Tetracycline bound to the 30S head
Analyse Tetracycline bound to the 30S head in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8CF1
- Type
- protein + RNA
- Length
- 1,473 residues
- Chains
- 10
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.82
- Source
- Escherichia coli BW25113
- Molecule
- 16S rRNA; 30S ribosomal protein S2; Small ribosomal subunit protein uS3; Small ribosomal…
- UniProt
- P0A7V0, P0A7V3, P0A7W1, P02359, P0A7X3, P0A7R5, P0A7S9, P0AG59, P0A7U3
- Ligands
- TAC, MG, K
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · resolution 1.82 · 10 distinct chains · 42% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 16S rRNA | rna | 485 | — | — |
| B | 30S ribosomal protein S2 | protein | 66 | 50% helix, 0% strand | P0A7V0 |
| C | Small ribosomal subunit protein uS3 | protein | 206 | 38% helix, 32% strand | P0A7V3 |
| E | Small ribosomal subunit protein uS5 | protein | 50 | 28% helix, 52% strand | P0A7W1 |
| G | 30S ribosomal protein S7 | protein | 146 | 55% helix, 10% strand | P02359 |
| I | Small ribosomal subunit protein uS9 | protein | 125 | 38% helix, 23% strand | P0A7X3 |
| J | Small ribosomal subunit protein uS10 | protein | 96 | 23% helix, 49% strand | P0A7R5 |
| M | Small ribosomal subunit protein uS13 | protein | 115 | 51% helix, 5% strand | P0A7S9 |
| N | Small ribosomal subunit protein uS14 | protein | 100 | 56% helix, 6% strand | P0AG59 |
| S | Small ribosomal subunit protein uS19 | protein | 84 | 31% helix, 18% strand | P0A7U3 |
Ligands and binding sites
- TAC · Tetracycline · ligand · chains A
- MG · Magnesium ion · metal · 31 copies · chains A, J, M, N, S
- K · Potassium ion · metal · 12 copies · chains A, 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 | 816 | 0.87 | 0.90 | 95 | MG, K |
| 2 | 690 | 0.85 | 0.90 | 52 | MG |
| 3 | 1114 | 0.83 | 0.85 | 78 | MG, K |
| 4 | 844 | 0.82 | 0.86 | 75 | MG |
| 5 | 335 | 0.76 | 0.88 | 51 | empty |
Interfaces
19 interfaces between chains.
- A–I · 2810 Ų buried · 80 hydrogen bonds · protein-nucleic
- A–N · 2367 Ų buried · 69 hydrogen bonds · protein-nucleic
- A–M · 1970 Ų buried · 56 hydrogen bonds · protein-nucleic
- A–G · 1908 Ų buried · 55 hydrogen bonds · protein-nucleic
- A–J · 1765 Ų buried · 51 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification).
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 P0A7V0
- Every structure of UniProt P0A7V3
- Every structure of UniProt P0A7W1
- Every structure of UniProt P02359
- Every structure of UniProt P0A7X3
- Every structure of UniProt P0A7R5
- Every structure of UniProt P0A7S9
- Every structure of UniProt P0AG59
- Every structure of UniProt P0A7U3
- Elsewhere: RCSB PDB 8CF1 · PDBe 8CF1 · UniProt P0A7V0 · UniProt P0A7V3 · UniProt P0A7W1 · UniProt P02359 · UniProt P0A7X3 · UniProt P0A7R5 · UniProt P0A7S9 · UniProt P0AG59 · UniProt P0A7U3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.