MolNFT v1 · #176814 · protein
Crystal structure of MERS-cov N-ntd complexed with ligand P4-2
7DYD · Nucleoprotein: “Crystal structure of MERS-cov N-ntd complexed with ligand P4-2”. X-ray diffraction, 1 ligand (EY3), 2 pockets (best druggability 0.66). MolNFT v1 #176814 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7DYD
- Type
- protein
- Length
- 483 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein
- UniProt
- A0A2I2MQD0
- Ligands
- EY3
- Pockets
- 2 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nucleoprotein | protein | 129 | 5% helix, 26% strand | A0A2I2MQD0 |
| B | Nucleoprotein | protein | 129 | 2% helix, 27% strand | A0A2I2MQD0 |
| C | Nucleoprotein | protein | 115 | 5% helix, 22% strand | A0A2I2MQD0 |
| D | Nucleoprotein | protein | 110 | 8% helix, 19% strand | A0A2I2MQD0 |
Ligands and binding sites
- EY3 · 5-propan-2-yloxy-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 | 424 | 0.66 | 0.79 | 54 | empty |
| 2 | 87 | 0.41 | 0.79 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–C · 556 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 551 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 318 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 7DYD · Crystal structure of MERS-CoV N-NTD complexed with ligand P4-2 · 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 7DYD · PDBe 7DYD · UniProt A0A2I2MQD0
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