MolNFT v1 · #182676 · protein
Structure of the SARS-cov-2 N protein C-terminal domain bound to single-domain antibody E2
7N0I · Nucleoprotein: “Structure of the SARS-cov-2 N protein C-terminal domain bound to single-domain antibody E2”. X-ray diffraction, 1 ligand (MG), 12 pockets (best druggability 0.82). MolNFT v1 #182676 on GenesisL1: 3D structure…
- PDB
- 7N0I
- Type
- protein
- Length
- 1,300 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nucleoprotein; Single-domain antibody E2
- UniProt
- P0DTC9
- Ligands
- MG
- Pockets
- 12 · best druggability 0.82
Structure
x-ray diffraction · 5 distinct chains · 16% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D, E, F, H, G | Nucleoprotein | protein | 96 | 43% helix, 22% strand | P0DTC9 |
| I | Single-domain antibody E2 | protein | 136 | 13% helix, 43% strand | — |
| J | Single-domain antibody E2 | protein | 135 | 12% helix, 45% strand | — |
| K | Single-domain antibody E2 | protein | 130 | 9% helix, 48% strand | — |
| L | Single-domain antibody E2 | protein | 131 | 9% helix, 47% strand | — |
Ligands and binding sites
- MG · Magnesium ion · metal · chains D, L
- ACT · Acetate ion · additive · 2 copies · chains C, D, H, L, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 842 | 0.82 | 0.85 | 92 | empty |
| 2 | 827 | 0.82 | 0.85 | 96 | ACT, MG |
| 3 | 333 | 0.69 | 0.83 | 50 | empty |
| 4 | 207 | 0.66 | 0.85 | 44 | empty |
| 5 | 396 | 0.63 | 0.78 | 41 | ACT |
Interfaces
27 interfaces between chains.
- H–G · 2199 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2112 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2106 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 2097 Ų buried · 26 hydrogen bonds · protein-protein
- E–K · 580 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7N0I · Structure of the SARS-CoV-2 N protein C-terminal domain bound to single-domain antibody E2 · 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 P0DTC9
- Elsewhere: RCSB PDB 7N0I · PDBe 7N0I · UniProt P0DTC9
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