MolNFT v1 · #23496 · protein + RNA
Crystal structure of a complex between wt bacteriophage MS2 coat protein and an F5 aptamer RNA stemloop with 2AMINOPURINE substituted at the-10 position
1U1Y: “Crystal structure of a complex between wt bacteriophage MS2 coat protein and an F5 aptamer RNA stemloop with…”. X-ray diffraction, 6 pockets (best druggability 0.75). MolNFT v1 #23496 on GenesisL1: 3D structure, binding sites and…
- PDB
- 1U1Y
- Type
- protein + RNA
- Length
- 419 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Coat protein; 5'-R(*CP*CP*GP*GP*(2PR) P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3'
- UniProt
- P03612
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Coat protein | protein | 129 | 19% helix, 47% strand | P03612 |
| R | 5'-R(*CP*CP*GP*GP*(2PR) P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*GP*G)-3' | rna | 16 | — | — |
| S | 5'-R(*CP*CP*GP*GP*(2PR) P*GP*GP*AP*UP*CP*AP*CP*CP*AP*CP*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 | 636 | 0.75 | 0.81 | 80 | empty |
| 2 | 333 | 0.57 | 0.76 | 34 | empty |
| 3 | 315 | 0.52 | 0.74 | 23 | empty |
| 4 | 83 | 0.48 | 0.82 | 18 | empty |
| 5 | 205 | 0.48 | 0.75 | 30 | empty |
Interfaces
5 interfaces between chains.
- B–C · 566 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 555 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 523 Ų buried · 5 hydrogen bonds · protein-protein
- C–S · 434 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–R · 420 Ų buried · 13 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1U1Y · Crystal structure of a complex between WT bacteriophage MS2 coat protein and an F5… · 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 1U1Y · PDBe 1U1Y · UniProt P03612
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