Research workbench
Bacterial 30S ribosomal subunit assembly complex state a (head domain)
Analyse Bacterial 30S ribosomal subunit assembly complex state a (head domain) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7AFD
- Type
- protein + RNA
- Length
- 1,564 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16SRRNA of the head domain (residue C931 to G1386); 30S ribosomal protein S2; 30S…
- UniProt
- C3TPN2, C3SQX2, A0A5Q2GFB5, C3SRY2, C3SQT7, C3SR52, C3SR07, C3SQW2
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 9 distinct chains · 42% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | 16SRRNA of the head domain (residue C931 to G1386) | rna | 456 | — | — |
| B | 30S ribosomal protein S2 | protein | 224 | 50% helix, 14% strand | C3TPN2 |
| C | 30S ribosomal protein S3 | protein | 211 | 36% helix, 27% strand | C3SQX2 |
| G | 30S ribosomal protein S7 | protein | 151 | 55% helix, 4% strand | A0A5Q2GFB5 |
| I | 30S ribosomal protein S9 | protein | 127 | 38% helix, 20% strand | C3SRY2 |
| J | 30S ribosomal protein S10 | protein | 99 | 24% helix, 44% strand | C3SQT7 |
| M | 30S ribosomal protein S13 | protein | 114 | 49% helix, 0% strand | C3SR52 |
| N | 30S ribosomal protein S14 | protein | 100 | 52% helix, 4% strand | C3SR07 |
| S | 30S ribosomal protein S19 | protein | 82 | 20% 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.85 | 0.88 | 54 | MG |
| 2 | 1161 | 0.84 | 0.85 | 96 | MG |
| 3 | 964 | 0.84 | 0.86 | 81 | MG |
| 4 | 976 | 0.83 | 0.85 | 91 | empty |
| 5 | 576 | 0.77 | 0.84 | 55 | empty |
Interfaces
17 interfaces between chains.
- 1–I · 2891 Ų buried · 100 hydrogen bonds · protein-nucleic
- 1–N · 2201 Ų buried · 66 hydrogen bonds · protein-nucleic
- 1–G · 1935 Ų buried · 72 hydrogen bonds · protein-nucleic
- 1–M · 1878 Ų buried · 74 hydrogen bonds · protein-nucleic
- 1–J · 1700 Ų buried · 40 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 7AFD · Bacterial 30S ribosomal subunit assembly complex state A (head domain) · 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 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 7AFD · PDBe 7AFD · UniProt C3TPN2 · UniProt C3SQX2 · UniProt A0A5Q2GFB5 · UniProt C3SRY2 · UniProt C3SQT7 · UniProt C3SR52 · UniProt C3SR07 · UniProt C3SQW2
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