Research workbench
SARS-cov-2 spike protein N terminal domain in complex with N11 Fab
Analyse SARS-cov-2 spike protein N terminal domain in complex with N11 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7E7X
- Type
- protein
- Length
- 1,280 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; N11 Fab heavy chain; N11 Fab light chain
- UniProt
- P0DTC2
- Pockets
- 16 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 230 | 0% helix, 53% strand | P0DTC2 |
| H, M | N11 Fab heavy chain | protein | 211 | 8% helix, 51% strand | — |
| L, N | N11 Fab light chain | protein | 211 | 6% helix, 51% strand | — |
| B | Spike protein S1 | protein | 206 | 1% helix, 51% strand | P0DTC2 |
Pockets
16 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 124 | 0.76 | 0.95 | 29 | empty |
| 2 | 568 | 0.61 | 0.74 | 63 | empty |
| 3 | 556 | 0.60 | 0.74 | 58 | empty |
| 4 | 296 | 0.53 | 0.74 | 32 | empty |
| 5 | 164 | 0.50 | 0.78 | 29 | empty |
Interfaces
10 interfaces between chains.
- H–L · 1719 Ų buried · 14 hydrogen bonds · protein-protein
- M–N · 1695 Ų buried · 14 hydrogen bonds · protein-protein
- A–H · 885 Ų buried · 13 hydrogen bonds · protein-protein
- B–M · 874 Ų buried · 11 hydrogen bonds · protein-protein
- H–M · 444 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 7E7X · SARS-CoV-2 Spike Protein N terminal domain in Complex with N11 Fab · 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 P0DTC2
- Elsewhere: RCSB PDB 7E7X · PDBe 7E7X · UniProt P0DTC2
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