Research workbench
SARS-cov-2 spike (2P) in complex with C12C9 Fab (ntd local reconstruction)
Analyse SARS-cov-2 spike (2P) in complex with C12C9 Fab (ntd local reconstruction) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N62
- Type
- protein
- Length
- 712 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C12C9 Fab heavy chain; C12C9 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.62
Structure
electron microscopy · 3 distinct chains · 4% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 277 | 0% helix, 36% strand | P0DTC2 |
| H | C12C9 Fab heavy chain | protein | 223 | 4% helix, 46% strand | — |
| L | C12C9 Fab light chain | protein | 212 | 8% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 79 | 0.62 | 0.90 | 25 | empty |
| 2 | 425 | 0.56 | 0.74 | 53 | empty |
| 3 | 121 | 0.40 | 0.75 | 25 | empty |
| 4 | 65 | 0.39 | 0.80 | 15 | empty |
| 5 | 52 | 0.35 | 0.78 | 12 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1697 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 757 Ų buried · 13 hydrogen bonds · protein-protein
- A–L · 104 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan (disulfide, N-glycosylation).
Compared structures
- 7N62 · SARS-CoV-2 Spike (2P) in complex with C12C9 Fab (NTD local reconstruction) · 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 7N62 · PDBe 7N62 · UniProt P0DTC2
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