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
- 7MSF
- Type
- protein + RNA
- Length
- 412 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- MS2 protein capsid; 5'-R(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)- 3'
- UniProt
- P03612
- Pockets
- 6 · best druggability 0.76
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(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)- 3' | rna | 14 | — | — |
| S | 5'-R(*UP*CP*GP*CP*CP*AP*AP*CP*AP*GP*GP*CP*GP*G)- 3' | rna | 11 | — | — |
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 702 | 0.76 | 0.81 | 96 | empty |
| 2 | 219 | 0.59 | 0.80 | 31 | empty |
| 3 | 197 | 0.42 | 0.73 | 20 | empty |
| 4 | 129 | 0.40 | 0.75 | 23 | empty |
| 5 | 75 | 0.32 | 0.74 | 17 | empty |
Interfaces
5 interfaces between chains.
- B–C · 548 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 544 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 512 Ų buried · 6 hydrogen bonds · protein-protein
- A–R · 416 Ų buried · 13 hydrogen bonds · protein-nucleic
- C–S · 361 Ų buried · 8 hydrogen bonds · protein-nucleic
Compared structures
- 7MSF · 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 7MSF · PDBe 7MSF · UniProt P03612
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