Research workbench
Mycoplasma pneumoniae 30S subunit of ribosomes in chloramphenicol- treated cells
Analyse Mycoplasma pneumoniae 30S subunit of ribosomes in chloramphenicol- treated cells in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7OOC
- Type
- protein + RNA
- Length
- 3,964 residues
- Chains
- 21
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 30S ribosomal protein S3; 30S ribosomal protein S5; 30S ribosomal protein S7; 30S…
- UniProt
- P41205, Q50301, P75545, P75560, P75179, Q50296, P46775, P75237, A0A0H3DLS7, P75546, Q50305, P75581, Q50297, P75173, P75576, P57079, Q50304, P75541, P75543, Q50309
- Ligands
- ZN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 21 distinct chains · 34% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | 30S ribosomal protein S3 | protein | 215 | 33% helix, 25% strand | P41205 |
| D | 30S ribosomal protein S5 | protein | 153 | 27% helix, 25% strand | Q50301 |
| F | 30S ribosomal protein S7 | protein | 154 | 53% helix, 6% strand | P75545 |
| A | 30S ribosomal protein S2 | protein | 249 | 39% helix, 6% strand | P75560 |
| H | 30S ribosomal protein S9 | protein | 128 | 30% helix, 9% strand | P75179 |
| J | 30S ribosomal protein S11 | protein | 114 | 27% helix, 25% strand | Q50296 |
| C | 30S ribosomal protein S4 | protein | 203 | 38% helix, 7% strand | P46775 |
| S | 30S ribosomal protein S20 | protein | 77 | 78% helix, 0% strand | P75237 |
| O | 30S ribosomal protein S16 | protein | 87 | 28% helix, 14% strand | A0A0H3DLS7 |
| K | 30S ribosomal protein S12 | protein | 136 | 3% helix, 25% strand | P75546 |
| M | 30S ribosomal protein S14 type Z | protein | 60 | 30% helix, 7% strand | Q50305 |
| I | 30S ribosomal protein S10 | protein | 101 | 19% helix, 29% strand | P75581 |
| L | 30S ribosomal protein S13 | protein | 118 | 42% helix, 2% strand | Q50297 |
| N | 30S ribosomal protein S15 | protein | 83 | 71% helix, 0% strand | P75173 |
| R | 30S ribosomal protein S19 | protein | 84 | 18% helix, 14% strand | P75576 |
| T | 30S ribosomal protein S21 | protein | 53 | 66% helix, 2% strand | P57079 |
| G | 30S ribosomal protein S8 | protein | 141 | 26% helix, 24% strand | Q50304 |
| Q | 30S ribosomal protein S18 | protein | 65 | 54% helix, 3% strand | P75541 |
| E | 30S ribosomal protein S6 | protein | 167 | 21% helix, 15% strand | P75543 |
| P | 30S ribosomal protein S17 | protein | 83 | 0% helix, 47% strand | Q50309 |
| 5 | 16S rRNA | rna | 1493 | — | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains M, Q
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 | 977 | 0.86 | 0.88 | 97 | empty |
| 2 | 942 | 0.86 | 0.88 | 91 | empty |
| 3 | 830 | 0.84 | 0.87 | 61 | empty |
| 4 | 929 | 0.84 | 0.86 | 78 | empty |
| 5 | 1161 | 0.83 | 0.85 | 92 | empty |
Interfaces
41 interfaces between chains.
- K–5 · 3386 Ų buried · 85 hydrogen bonds · protein-nucleic
- H–5 · 2961 Ų buried · 55 hydrogen bonds · protein-nucleic
- C–5 · 2952 Ų buried · 72 hydrogen bonds · protein-nucleic
- S–5 · 2472 Ų buried · 53 hydrogen bonds · protein-nucleic
- O–5 · 2403 Ų buried · 39 hydrogen bonds · protein-nucleic
Compared structures
- 7OOC · Mycoplasma pneumoniae 30S subunit of ribosomes in chloramphenicol-treated cells · the same entry in another collection · chain S against S, 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 P41205
- Every structure of UniProt Q50301
- Every structure of UniProt P75545
- Every structure of UniProt P75560
- Every structure of UniProt P75179
- Every structure of UniProt Q50296
- Every structure of UniProt P46775
- Every structure of UniProt P75237
- Every structure of UniProt A0A0H3DLS7
- Every structure of UniProt P75546
- Every structure of UniProt Q50305
- Every structure of UniProt P75581
- Every structure of UniProt Q50297
- Every structure of UniProt P75173
- Every structure of UniProt P75576
- Every structure of UniProt P57079
- Every structure of UniProt Q50304
- Every structure of UniProt P75541
- Every structure of UniProt P75543
- Every structure of UniProt Q50309
- Elsewhere: RCSB PDB 7OOC · PDBe 7OOC · UniProt P41205 · UniProt Q50301 · UniProt P75545 · UniProt P75560 · UniProt P75179 · UniProt Q50296 · UniProt P46775 · UniProt P75237 · UniProt A0A0H3DLS7 · UniProt P75546 · UniProt Q50305 · UniProt P75581 · UniProt Q50297 · UniProt P75173 · UniProt P75576 · UniProt P57079 · UniProt Q50304 · UniProt P75541 · UniProt P75543 · UniProt Q50309
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