MolNFT v1 · #182951 · protein
Cryoem structure of SARS-cov-2 spike in complex with NB17
7N9T · Spike glycoprotein: “Cryoem structure of SARS-cov-2 spike in complex with NB17”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #182951 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7N9T
- Type
- protein
- Length
- 3,726 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Nanobody NB17
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 2 distinct chains · 19% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1123 | 20% helix, 22% strand | P0DTC2 |
| D, E, F | Nanobody NB17 | protein | 119 | 3% helix, 34% strand | — |
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 | 836 | 0.88 | 0.91 | 113 | empty |
| 2 | 1118 | 0.87 | 0.87 | 133 | empty |
| 3 | 1057 | 0.86 | 0.87 | 129 | empty |
| 4 | 1173 | 0.85 | 0.86 | 126 | empty |
| 5 | 653 | 0.84 | 0.89 | 84 | empty |
Interfaces
9 interfaces between chains.
- A–C · 4456 Ų buried · 29 hydrogen bonds · protein-protein
- B–C · 4378 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 4361 Ų buried · 30 hydrogen bonds · protein-protein
- B–F · 704 Ų buried · 9 hydrogen bonds · protein-protein
- A–E · 670 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 33 disulfide (disulfide).
Compared structures
- 7N9T · CryoEM structure of SARS-CoV-2 Spike in complex with Nb17 · 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 7N9T · PDBe 7N9T · UniProt P0DTC2
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