MolNFT v1 · #172280 · protein
Cryo-EM structure of the SARS-cov-2 spike protein bound to neutralizing nanobodies (TY1)
6ZXN · Spike glycoprotein: “Cryo-EM structure of the SARS-cov-2 spike protein bound to neutralizing nanobodies (TY1)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #172280 on GenesisL1: 3D structure…
- PDB
- 6ZXN
- Type
- protein
- Length
- 3,522 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Nanobody TY1
- 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 | Spike glycoprotein | protein | 1060 | 21% helix, 33% strand | P0DTC2 |
| B, C | Spike glycoprotein | protein | 1054 | 21% helix, 35% strand | P0DTC2 |
| D, E, F | Nanobody TY1 | protein | 118 | 5% helix, 37% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 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 | 822 | 0.85 | 0.87 | 85 | empty |
| 2 | 651 | 0.84 | 0.88 | 66 | empty |
| 3 | 1017 | 0.83 | 0.84 | 120 | empty |
| 4 | 912 | 0.81 | 0.83 | 89 | empty |
| 5 | 1136 | 0.79 | 0.81 | 103 | empty |
Interfaces
7 interfaces between chains.
- B–C · 4844 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 4828 Ų buried · 48 hydrogen bonds · protein-protein
- A–B · 4557 Ų buried · 42 hydrogen bonds · protein-protein
- C–F · 941 Ų buried · 15 hydrogen bonds · protein-protein
- B–E · 862 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 glycan, 42 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ZXN · Cryo-EM structure of the SARS-CoV-2 spike protein bound to neutralizing nanobodies (Ty1) · 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 6ZXN · PDBe 6ZXN · UniProt P0DTC2
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