MolNFT v1 · #172835 · protein + RNA
Bacterial 30S ribosomal subunit assembly complex state D (head domain)
7AFK · 16SRRNA (head domain of the 30S ribosome): “Bacterial 30S ribosomal subunit assembly complex state D (head domain)”. Electron microscopy, 2 ligands (MG, ZN), 20 pockets (best druggability 0.85). MolNFT v1 #172835 on GenesisL1: 3D…
- PDB
- 7AFK
- Type
- protein + RNA
- Length
- 1,564 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 16SRRNA (head domain of the 30S ribosome); 30S ribosomal protein S2; 30S ribosomal…
- UniProt
- C3TPN2, C3SQX2, A0A5Q2GFB5, C3SRY2, C3SQT7, C3SR52, C3SR07, C3SQW2
- Ligands
- MG, ZN
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 9 distinct chains · 41% helix, 16% 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 | 33% helix, 27% strand | C3SQX2 |
| G | 30S ribosomal protein S7 | protein | 151 | 56% helix, 3% strand | A0A5Q2GFB5 |
| I | 30S ribosomal protein S9 | protein | 127 | 35% helix, 21% strand | C3SRY2 |
| J | 30S ribosomal protein S10 | protein | 99 | 25% helix, 36% strand | C3SQT7 |
| M | 30S ribosomal protein S13 | protein | 114 | 51% helix, 0% strand | C3SR52 |
| N | 30S ribosomal protein S14 | protein | 100 | 49% helix, 2% strand | C3SR07 |
| S | 30S ribosomal protein S19 | protein | 82 | 16% 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 | 916 | 0.85 | 0.87 | 58 | MG |
| 2 | 961 | 0.84 | 0.86 | 86 | empty |
| 3 | 797 | 0.82 | 0.86 | 63 | MG |
| 4 | 586 | 0.82 | 0.87 | 48 | empty |
| 5 | 959 | 0.82 | 0.84 | 70 | empty |
Interfaces
17 interfaces between chains.
- 1–I · 2736 Ų buried · 107 hydrogen bonds · protein-nucleic
- 1–N · 2197 Ų buried · 77 hydrogen bonds · protein-nucleic
- 1–G · 2002 Ų buried · 81 hydrogen bonds · protein-nucleic
- 1–M · 1810 Ų buried · 75 hydrogen bonds · protein-nucleic
- 1–J · 1666 Ų buried · 50 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 modified (nucleotide modification).
Compared structures
- 7AFK · Bacterial 30S ribosomal subunit assembly complex state D (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 7AFK · PDBe 7AFK · UniProt C3TPN2 · UniProt C3SQX2 · UniProt A0A5Q2GFB5 · UniProt C3SRY2 · UniProt C3SQT7 · UniProt C3SR52 · UniProt C3SR07 · UniProt C3SQW2
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