Research workbench
Bacteriophage MS2 capsid PROTEIN/RNA complex
Analyse Bacteriophage MS2 capsid PROTEIN/RNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1AQ3
- Type
- protein + RNA
- Length
- 415 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RNA (5'- R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*U P*GP*U)-3'); Protein…
- UniProt
- P03612
- Pockets
- 5 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| R | RNA (5'- R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*U P*GP*U)-3') | rna | 16 | — | — |
| S | RNA (5'- R(*AP*CP*AP*UP*GP*AP*GP*GP*AP*UP*UP*AP*CP*CP*CP*AP*U P*GP*U)-3') | rna | 12 | — | — |
| A, B, C | Protein (bacteriophage MS2 coat protein) | protein | 129 | 19% helix, 46% strand | P03612 |
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1000 | 0.76 | 0.78 | 119 | empty |
| 2 | 364 | 0.59 | 0.76 | 34 | empty |
| 3 | 233 | 0.50 | 0.75 | 30 | empty |
| 4 | 193 | 0.42 | 0.73 | 21 | empty |
| 5 | 113 | 0.34 | 0.73 | 15 | empty |
Interfaces
5 interfaces between chains.
- B–C · 558 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 546 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 521 Ų buried · 5 hydrogen bonds · protein-protein
- R–A · 431 Ų buried · 11 hydrogen bonds · protein-nucleic
- S–C · 358 Ų buried · 9 hydrogen bonds · protein-nucleic
Compared structures
- 1AQ3 · Bacteriophage MS2 capsid PROTEIN/RNA 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 1AQ3 · PDBe 1AQ3 · UniProt P03612
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