Research workbench
Crystal structure of MERS-CoV N-NTD complexed with ligand P4-4
Analyse Crystal structure of MERS-CoV N-NTD complexed with ligand P4-4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LZ8
- Type
- protein
- Length
- 480 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.59
- Source
- Middle East respiratory syndrome-related coronavirus
- Molecule
- Nucleoprotein
- UniProt
- A0A2I2MQD0
- Ligands
- EY9
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.59 · 4 distinct chains · 5% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 128 | 5% helix, 26% strand | A0A2I2MQD0 |
| C | Nucleoprotein | protein | 110 | 5% helix, 22% strand | A0A2I2MQD0 |
| B | Nucleoprotein | protein | 130 | 5% helix, 25% strand | A0A2I2MQD0 |
| D | Nucleoprotein | protein | 112 | 5% helix, 22% strand | A0A2I2MQD0 |
Ligands and binding sites
- EY9 · 5-(2-methoxyethoxy)-1H-indole · ligand · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.64 | 0.79 | 50 | empty |
| 2 | 70 | 0.41 | 0.80 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–D · 580 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 563 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 310 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6LZ8 · Crystal structure of MERS-cov N-ntd complexed with ligand P4-4 · 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 A0A2I2MQD0
- Elsewhere: RCSB PDB 6LZ8 · PDBe 6LZ8 · UniProt A0A2I2MQD0
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