MolNFT v1 · #29597 · protein + RNA
RNA bacteriophage MS2 coat PROTEIN/RNA complex
1ZDI · Protein (RNA bacteriophage MS2 coat protein): “RNA bacteriophage MS2 coat PROTEIN/RNA complex”. X-ray diffraction, 4 pockets (best druggability 0.76). MolNFT v1 #29597 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 1ZDI
- Type
- protein + RNA
- Length
- 416 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (RNA bacteriophage MS2 coat protein); RNA (5'…
- UniProt
- P03612
- Pockets
- 4 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 19% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Protein (RNA bacteriophage MS2 coat protein) | protein | 129 | 19% helix, 46% strand | P03612 |
| 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 | 13 | — | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1058 | 0.76 | 0.78 | 133 | empty |
| 2 | 357 | 0.58 | 0.76 | 33 | empty |
| 3 | 231 | 0.46 | 0.74 | 23 | empty |
| 4 | 90 | 0.31 | 0.73 | 14 | empty |
Interfaces
5 interfaces between chains.
- B–C · 565 Ų buried · 11 hydrogen bonds · protein-protein
- A–B · 545 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 525 Ų buried · 4 hydrogen bonds · protein-protein
- A–R · 444 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–S · 360 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 1ZDI · RNA bacteriophage MS2 coat 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 1ZDI · PDBe 1ZDI · UniProt P03612
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.