Research workbench
Crystal structure of MERS-cov N-ntd complexed with 5-benzyloxygramine
Analyse Crystal structure of MERS-cov N-ntd complexed with 5-benzyloxygramine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KL6
- Type
- protein
- Length
- 453 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- UniProt
- A0A0D3MU65
- Ligands
- DJU
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 4 distinct chains · 3% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 117 | 3% helix, 23% strand | A0A0D3MU65 |
| B | Nucleoprotein | protein | 116 | 3% helix, 23% strand | A0A0D3MU65 |
| C | Nucleoprotein | protein | 109 | 3% helix, 23% strand | A0A0D3MU65 |
| D | Nucleoprotein | protein | 111 | 3% helix, 22% strand | A0A0D3MU65 |
Ligands and binding sites
- DJU · N,N-dimethyl-1-(5-phenylmethoxy-1H-indol-3-yl) methanamine · ligand · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 304 | 0.64 | 0.81 | 39 | empty |
| 2 | 242 | 0.57 | 0.78 | 28 | DJU |
| 3 | 84 | 0.48 | 0.82 | 20 | empty |
| 4 | 76 | 0.45 | 0.82 | 19 | empty |
| 5 | 67 | 0.29 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–C · 542 Ų buried · 2 hydrogen bonds · protein-protein
- A–B · 344 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 303 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6KL6 · Crystal structure of MERS-CoV N-NTD complexed with 5-Benzyloxygramine · 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 A0A0D3MU65
- Elsewhere: RCSB PDB 6KL6 · PDBe 6KL6 · UniProt A0A0D3MU65
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.