Research workbench
Ribosome-secy complex
Analyse Ribosome-secy complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BO0
- Type
- protein + RNA
- Length
- 644 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 23S ribosomal RNA; Preprotein translocase secy subunit; Preprotein translocase sece…
- Pockets
- 11 · best druggability 0.77
Structure
electron microscopy · 7 distinct chains · 56% helix, 1% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D | 23S ribosomal RNA | rna | 27 | — | — |
| E | 23S ribosomal RNA | rna | 27 | — | — |
| F | 23S ribosomal RNA | rna | 19 | — | — |
| G | 23S ribosomal RNA | rna | 32 | — | — |
| A | Preprotein translocase secy subunit | protein | 442 | 54% helix, 1% strand | — |
| B | Preprotein translocase sece subunit | protein | 65 | 74% helix, 0% strand | — |
| C | Preprotein translocase secg subunit | protein | 32 | 53% helix, 3% strand | — |
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 836 | 0.77 | 0.81 | 84 | empty |
| 2 | 855 | 0.73 | 0.77 | 100 | empty |
| 3 | 379 | 0.66 | 0.80 | 43 | empty |
| 4 | 321 | 0.58 | 0.76 | 36 | empty |
| 5 | 157 | 0.56 | 0.80 | 20 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1602 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 1339 Ų buried · 11 hydrogen bonds · protein-protein
- D–A · 120 Ų buried · 2 hydrogen bonds · protein-nucleic
- G–A · 118 Ų buried · 0 hydrogen bonds · protein-nucleic
- F–G · 107 Ų buried · 1 hydrogen bond · nucleic-nucleic
Compared structures
- 3BO0 · Ribosome-SecY complex · the same entry in another collection · chain D against D, 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
- Elsewhere: RCSB PDB 3BO0 · PDBe 3BO0
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