Research workbench
MS2 protein CAPSID/RNA complex
Analyse MS2 protein CAPSID/RNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MSF
- Type
- protein + RNA
- Length
- 421 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MS2 protein capsid; 5'- R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)- 3'
- UniProt
- P03612
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | MS2 protein capsid | protein | 129 | 19% helix, 47% strand | P03612 |
| R | 5'- R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)- 3' | rna | 18 | — | — |
| S | 5'- R(*CP*CP*GP*GP*AP*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*GP*G)- 3' | rna | 16 | — | — |
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1093 | 0.77 | 0.79 | 130 | empty |
| 2 | 560 | 0.63 | 0.76 | 57 | empty |
| 3 | 328 | 0.54 | 0.75 | 23 | empty |
| 4 | 203 | 0.48 | 0.76 | 27 | empty |
| 5 | 55 | 0.47 | 0.85 | 18 | empty |
Interfaces
5 interfaces between chains.
- B–C · 566 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 555 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 528 Ų buried · 6 hydrogen bonds · protein-protein
- A–R · 434 Ų buried · 16 hydrogen bonds · protein-nucleic
- C–S · 413 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 5MSF · MS2 protein CAPSID/RNA complex · the same entry in another collection · chain R against R, 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 5MSF · PDBe 5MSF · UniProt P03612
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