MolNFT v1 · #164412 · protein + RNA
Specific dsrna recognition by wild type H7N1 NS1 RNA-binding domain
6SX0 · Non-structural protein 1: “Specific dsrna recognition by wild type H7N1 NS1 RNA-binding domain”. X-ray diffraction, 3 pockets (best druggability 0.75). MolNFT v1 #164412 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6SX0
- Type
- protein + RNA
- Length
- 179 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Non-structural protein 1; RNA (5'- R(*GP*GP*UP*AP*AP*CP*UP*GP*UP*UP*AP*CP*AP*GP*UP*UP*AP*C…
- UniProt
- Q1PST0
- Pockets
- 3 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Non-structural protein 1 | protein | 70 | 86% helix, 0% strand | Q1PST0 |
| B | Non-structural protein 1 | protein | 71 | 85% helix, 0% strand | Q1PST0 |
| C, D | RNA (5'- R(*GP*GP*UP*AP*AP*CP*UP*GP*UP*UP*AP*CP*AP*GP*UP*UP*AP*CP*C)-3') | rna | 19 | — | — |
Ligands and binding sites
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 5 copies · chains A, D, B
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.75 | 0.79 | 56 | PE4 |
| 2 | 57 | 0.68 | 0.96 | 14 | empty |
| 3 | 54 | 0.67 | 0.97 | 13 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1096 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 830 Ų buried · 72 hydrogen bonds · nucleic-nucleic
- B–D · 378 Ų buried · 2 hydrogen bonds · protein-nucleic
- B–C · 339 Ų buried · 7 hydrogen bonds · protein-nucleic
- A–C · 317 Ų buried · 2 hydrogen bonds · protein-nucleic
Compared structures
- 6SX0 · Specific dsRNA recognition by wild type H7N1 NS1 RNA-binding domain · 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 Q1PST0
- Elsewhere: RCSB PDB 6SX0 · PDBe 6SX0 · UniProt Q1PST0
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