Research workbench
F6 aptamer MS2 coat protein complex
Analyse F6 aptamer MS2 coat protein complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MSF
- Type
- protein + RNA
- Length
- 411 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Enterobacterio phage MS2; SYNTHETIC CONSTRUCT
- Molecule
- RNA (5'-R(*CP*CP*AP*CP*AP*GP*UP*CP*AP*CP*UP*GP*GP*G)-3'); RNA…
- UniProt
- P03612
- Pockets
- 3 · best druggability 0.79
Structure
x-ray diffraction · resolution 2.8 · 3 distinct chains · 19% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | RNA (5'-R(*CP*CP*AP*CP*AP*GP*UP*CP*AP*CP*UP*GP*GP*G)-3') | rna | 14 | — | — |
| S | RNA (5'-R(*CP*AP*GP*UP*CP*AP*CP*UP*GP*G)-3') | rna | 10 | — | — |
| A, B, C | Protein (MS2 protein capsid) | protein | 129 | 19% helix, 47% strand | P03612 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 990 | 0.79 | 0.81 | 116 | empty |
| 2 | 171 | 0.41 | 0.73 | 15 | empty |
| 3 | 73 | 0.39 | 0.78 | 19 | empty |
Interfaces
5 interfaces between chains.
- B–C · 565 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 549 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 516 Ų buried · 6 hydrogen bonds · protein-protein
- S–C · 391 Ų buried · 10 hydrogen bonds · protein-nucleic
- R–A · 368 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 6MSF · F6 aptamer MS2 coat protein complex · the same entry in another collection · chain A against A, 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 P03612
- Elsewhere: RCSB PDB 6MSF · PDBe 6MSF · UniProt P03612
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