MolNFT v1 · #191272 · protein
SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 2-57
8CXN · Spike glycoprotein: “SARS-cov-2 spike protein in complex with a pan-sarbecovirus nanobody 2-57”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #191272 on GenesisL1: 3D structure, binding sites…
- PDB
- 8CXN
- Type
- protein
- Length
- 3,678 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Pan-sarbecovirus nanobody 2-57
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 2 distinct chains · 20% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1100 | 22% helix, 32% strand | P0DTC2 |
| D, F, E | Pan-sarbecovirus nanobody 2-57 | protein | 126 | 2% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 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 | 610 | 0.87 | 0.91 | 73 | empty |
| 2 | 637 | 0.81 | 0.86 | 82 | empty |
| 3 | 501 | 0.79 | 0.86 | 73 | empty |
| 4 | 127 | 0.78 | 0.96 | 22 | empty |
| 5 | 561 | 0.77 | 0.84 | 40 | empty |
Interfaces
7 interfaces between chains.
- B–C · 4883 Ų buried · 44 hydrogen bonds · protein-protein
- A–B · 4751 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 4615 Ų buried · 41 hydrogen bonds · protein-protein
- C–F · 1072 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 969 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 35 disulfide, 19 glycan (disulfide, N-glycosylation).
Compared structures
- 8CXN · SARS-CoV-2 Spike protein in complex with a pan-sarbecovirus nanobody 2-57 · 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 8CXN · PDBe 8CXN · UniProt P0DTC2
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