Research workbench
Bacterial 30S ribosomal subunit assembly complex state E (head domain)
Analyse Bacterial 30S ribosomal subunit assembly complex state E (head domain) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AF8
- Type
- protein + RNA
- Length
- 1,565 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.75
- Source
- Escherichia coli
- Molecule
- 16SrRNA (head domain of the 30S ribosome; 30S ribosomal protein S2; 30S ribosomal protein…
- UniProt
- C3TPN2, C3SQX2, A0A5Q2GFB5, C3SRY2, C3SQT7, C3SR52, C3SR07, C3SQW2
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 2.75 · 9 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | 16SrRNA (head domain of the 30S ribosome | rna | 456 | — | — |
| B | 30S ribosomal protein S2 | protein | 224 | 50% helix, 14% strand | C3TPN2 |
| C | 30S ribosomal protein S3 | protein | 211 | 36% helix, 30% strand | C3SQX2 |
| G | 30S ribosomal protein S7 | protein | 151 | 57% helix, 8% strand | A0A5Q2GFB5 |
| I | 30S ribosomal protein S9 | protein | 127 | 34% helix, 21% strand | C3SRY2 |
| J | 30S ribosomal protein S10 | protein | 99 | 26% helix, 35% strand | C3SQT7 |
| M | 30S ribosomal protein S13 | protein | 114 | 50% helix, 2% strand | C3SR52 |
| N | 30S ribosomal protein S14 | protein | 100 | 56% helix, 6% strand | C3SR07 |
| S | 30S ribosomal protein S19 | protein | 83 | 24% helix, 18% strand | C3SQW2 |
Ligands and binding sites
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 | 998 | 0.84 | 0.86 | 81 | MG |
| 2 | 657 | 0.84 | 0.89 | 48 | MG |
| 3 | 912 | 0.84 | 0.86 | 84 | MG |
| 4 | 1197 | 0.83 | 0.85 | 99 | MG |
| 5 | 600 | 0.81 | 0.87 | 74 | MG |
Interfaces
17 interfaces between chains.
- 1–I · 2983 Ų buried · 76 hydrogen bonds · protein-nucleic
- 1–N · 2355 Ų buried · 60 hydrogen bonds · protein-nucleic
- 1–G · 2013 Ų buried · 48 hydrogen bonds · protein-nucleic
- 1–M · 1910 Ų buried · 55 hydrogen bonds · protein-nucleic
- 1–J · 1821 Ų buried · 38 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 7AF8 · Bacterial 30S ribosomal subunit assembly complex state E (head domain) · the same entry in another collection · chain 1 against 1, 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 C3TPN2
- Every structure of UniProt C3SQX2
- Every structure of UniProt A0A5Q2GFB5
- Every structure of UniProt C3SRY2
- Every structure of UniProt C3SQT7
- Every structure of UniProt C3SR52
- Every structure of UniProt C3SR07
- Every structure of UniProt C3SQW2
- Elsewhere: RCSB PDB 7AF8 · PDBe 7AF8 · UniProt C3TPN2 · UniProt C3SQX2 · UniProt A0A5Q2GFB5 · UniProt C3SRY2 · UniProt C3SQT7 · UniProt C3SR52 · UniProt C3SR07 · UniProt C3SQW2
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