Research workbench
Cryoem structure of SARS-cov-2 spike protein (S-6P, 2-up) in complex with sybodies (SB45)
Analyse Cryoem structure of SARS-cov-2 spike protein (S-6P, 2-up) in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7N0H
- Type
- protein
- Length
- 3,469 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Synthetic nanobody (SB45)
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 20% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 1076 | 21% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1075 | 21% helix, 34% strand | P0DTC2 |
| X, Z | Synthetic nanobody (SB45) | protein | 121 | 2% helix, 57% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 64 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 572 | 0.85 | 0.90 | 88 | empty |
| 2 | 738 | 0.83 | 0.87 | 70 | empty |
| 3 | 725 | 0.83 | 0.87 | 100 | empty |
| 4 | 1036 | 0.77 | 0.79 | 92 | empty |
| 5 | 540 | 0.77 | 0.84 | 75 | empty |
Interfaces
7 interfaces between chains.
- A–C · 4716 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 4481 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 4455 Ų buried · 38 hydrogen bonds · protein-protein
- A–X · 1104 Ų buried · 15 hydrogen bonds · protein-protein
- C–Z · 1088 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 49 glycan, 41 disulfide (N-glycosylation, disulfide, glycation, glycosylation).
Compared structures
- 7N0H · CryoEM structure of SARS-CoV-2 spike protein (S-6P, 2-up) in complex with sybodies (Sb45) · 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 7N0H · PDBe 7N0H · UniProt P0DTC2
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