MolNFT v1 · #47026 · protein + RNA
Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors
2OM7 · Fragment of 16S rRNA (H14): “Structural basis for interaction of the ribosome with the switch regions of GTP-bound elongation factors”. Electron microscopy, 20 pockets (best druggability 0.79). MolNFT v1 #47026 on GenesisL1: 3D…
- PDB
- 2OM7
- Type
- protein + RNA
- Length
- 1,664 residues
- Chains
- 14
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fragment of 16S rRNA (H14); Fragment of 16S rRNA (H15); Fragment of 16S rRNA (H44); 16S…
- UniProt
- P17293, Q5SLP7, P13551, P80371
- Pockets
- 20 · best druggability 0.79
Structure
electron microscopy · 14 distinct chains · 26% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fragment of 16S rRNA (H14) | rna | 12 | — | — |
| B | Fragment of 16S rRNA (H15) | rna | 10 | — | — |
| C | Fragment of 16S rRNA (H44) | rna | 96 | — | — |
| D | 16S ribosomal RNA (H5) | rna | 13 | — | — |
| F | Fragment OF23S rRNA (H95) | rna | 29 | — | — |
| G | Fragment OF23S rRNA (H68) | rna | 54 | — | — |
| H | Fragment OF23S rRNA (H89) | rna | 42 | — | — |
| I | Fragment OF23S rRNA (H42-44) | rna | 58 | — | — |
| J | Fragment OF23S rRNA (H76) | rna | 73 | — | — |
| M | P/E-tRNA | rna | 74 | — | — |
| E | 30S ribosomal protein S12 | protein | 124 | 5% helix, 20% strand | P17293 |
| K | 50S ribosomal protein L1 | protein | 190 | 4% helix, 3% strand | Q5SLP7 |
| L | Elongation factor G | protein | 655 | 29% helix, 33% strand | P13551 |
| N | 30S ribosomal protein S2 | protein | 234 | 50% helix, 10% strand | P80371 |
Pockets
20 pockets found on a 1 Å grid, 15 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1104 | 0.79 | 0.81 | 123 | empty |
| 2 | 986 | 0.75 | 0.79 | 58 | empty |
| 3 | 426 | 0.71 | 0.82 | 42 | empty |
| 4 | 274 | 0.68 | 0.85 | 31 | empty |
| 5 | 727 | 0.67 | 0.76 | 35 | empty |
Interfaces
16 interfaces between chains.
- J–K · 849 Ų buried · 18 hydrogen bonds · protein-nucleic
- F–L · 723 Ų buried · 43 hydrogen bonds · protein-nucleic
- I–L · 431 Ų buried · 26 hydrogen bonds · protein-nucleic
- D–L · 302 Ų buried · 7 hydrogen bonds · protein-nucleic
- B–L · 291 Ų buried · 7 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 6 modified (nucleotide modification).
Compared structures
- 2OM7 · Structural Basis for Interaction of the Ribosome with the Switch Regions of GTP-bound… · the same entry in another collection · chain M against M, 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 P17293
- Every structure of UniProt Q5SLP7
- Every structure of UniProt P13551
- Every structure of UniProt P80371
- Elsewhere: RCSB PDB 2OM7 · PDBe 2OM7 · UniProt P17293 · UniProt Q5SLP7 · UniProt P13551 · UniProt P80371
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