MolNFT v2 · #213888 · protein
Crystal structure of SARS-CoV2 N-NTD complexed with 5-Benzyloxygramine derivative (P3-8)
8J6X · Nucleoprotein: “Crystal structure of SARS-CoV2 N-NTD complexed with 5-Benzyloxygramine derivative (P3-8)”. X-ray diffraction at 2.7, 1 ligand (U2H), 1 pocket (best druggability 0.83). MolNFT v2 #213888 on GenesisL1: 3D structure…
- PDB
- 8J6X
- Type
- protein
- Length
- 508 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.7
- Source
- Severe acute respiratory syndrome coronavirus 2
- Molecule
- Nucleoprotein
- UniProt
- P0DTC9
- Ligands
- U2H
- Pockets
- 1 · best druggability 0.83
Structure
x-ray diffraction · resolution 2.7 · 4 distinct chains · 1% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 126 | 2% helix, 25% strand | P0DTC9 |
| B | Nucleoprotein | protein | 128 | 0% helix, 24% strand | P0DTC9 |
| C | Nucleoprotein | protein | 127 | 2% helix, 24% strand | P0DTC9 |
| D | Nucleoprotein | protein | 127 | 0% helix, 27% strand | P0DTC9 |
Ligands and binding sites
- U2H · ~{N}-methyl-~{N}-[(5-phenylmethoxy-1~{H}-indol-3-yl)methyl]propan-1-amine · ligand · chains A, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1091 | 0.83 | 0.84 | 115 | U2H |
Interfaces
5 interfaces between chains.
- A–B · 537 Ų buried · 8 hydrogen bonds · protein-protein
- A–C · 394 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 349 Ų buried · 2 hydrogen bonds · protein-protein
- A–D · 339 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 176 Ų buried · 2 hydrogen bonds · protein-protein
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 P0DTC9
- Elsewhere: RCSB PDB 8J6X · PDBe 8J6X · UniProt P0DTC9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.