MolNFT v1 · #172828 · protein + RNA
Bacterial 30S ribosomal subunit assembly complex state M (head domain)
7AF3 · 16S rRNA (head): “Bacterial 30S ribosomal subunit assembly complex state M (head domain)”. Electron microscopy, 2 ligands (MG, ZN), 20 pockets (best druggability 0.86). MolNFT v1 #172828 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7AF3
- Type
- protein + RNA
- Length
- 1,567 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16S rRNA (head); 30S ribosomal protein S3; 30S ribosomal protein S7; 30S ribosomal…
- UniProt
- C3SQX2, A0A5Q2GFB5, C3SRY2, C3SQT7, C3SR52, C3SR07, C3SQW2, C3TPN2
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 9 distinct chains · 43% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| 1 | 16S rRNA (head) | rna | 456 | — | — |
| C | 30S ribosomal protein S3 | protein | 211 | 38% helix, 29% strand | C3SQX2 |
| G | 30S ribosomal protein S7 | protein | 151 | 55% helix, 4% strand | A0A5Q2GFB5 |
| I | 30S ribosomal protein S9 | protein | 127 | 33% helix, 22% strand | C3SRY2 |
| J | 30S ribosomal protein S10 | protein | 100 | 25% helix, 44% strand | C3SQT7 |
| M | 30S ribosomal protein S13 | protein | 115 | 50% helix, 2% strand | C3SR52 |
| N | 30S ribosomal protein S14 | protein | 100 | 52% helix, 6% strand | C3SR07 |
| S | 30S ribosomal protein S19 | protein | 83 | 27% helix, 18% strand | C3SQW2 |
| B | 30S ribosomal protein S2 | protein | 224 | 51% helix, 14% strand | C3TPN2 |
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 | 975 | 0.86 | 0.89 | 74 | MG |
| 2 | 1041 | 0.85 | 0.86 | 86 | MG |
| 3 | 839 | 0.83 | 0.86 | 71 | MG |
| 4 | 681 | 0.82 | 0.87 | 63 | MG |
| 5 | 664 | 0.80 | 0.85 | 56 | MG |
Interfaces
17 interfaces between chains.
- 1–I · 3019 Ų buried · 80 hydrogen bonds · protein-nucleic
- 1–N · 2304 Ų buried · 57 hydrogen bonds · protein-nucleic
- 1–G · 2023 Ų buried · 43 hydrogen bonds · protein-nucleic
- 1–M · 1962 Ų buried · 48 hydrogen bonds · protein-nucleic
- 1–J · 1733 Ų buried · 33 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 7AF3 · Bacterial 30S ribosomal subunit assembly complex state M (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 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
- Every structure of UniProt C3TPN2
- Elsewhere: RCSB PDB 7AF3 · PDBe 7AF3 · UniProt C3SQX2 · UniProt A0A5Q2GFB5 · UniProt C3SRY2 · UniProt C3SQT7 · UniProt C3SR52 · UniProt C3SR07 · UniProt C3SQW2 · UniProt C3TPN2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.