MolNFT v1 · #183042 · protein
EM structure of SARS-cov-2 spike glycoprotein in complex with covox-40 Fab
7ND3: “EM structure of SARS-cov-2 spike glycoprotein in complex with covox-40 Fab”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #183042 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7ND3
- Type
- protein
- Length
- 3,194 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Covox-40 heavy chain; Covox-40 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 995 | 24% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 989 | 24% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 991 | 24% helix, 32% strand | P0DTC2 |
| H | Covox-40 heavy chain | protein | 113 | 5% helix, 54% strand | — |
| L | Covox-40 light chain | protein | 106 | 3% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 49 copies · chains A, C, B
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 | 1056 | 0.87 | 0.89 | 129 | empty |
| 2 | 904 | 0.82 | 0.84 | 93 | empty |
| 3 | 426 | 0.79 | 0.88 | 46 | empty |
| 4 | 360 | 0.77 | 0.87 | 42 | empty |
| 5 | 269 | 0.75 | 0.88 | 36 | empty |
Interfaces
6 interfaces between chains.
- A–C · 5293 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 4787 Ų buried · 37 hydrogen bonds · protein-protein
- B–C · 4409 Ų buried · 33 hydrogen bonds · protein-protein
- B–H · 641 Ų buried · 16 hydrogen bonds · protein-protein
- H–L · 567 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 disulfide, 38 glycan (disulfide, N-glycosylation).
Compared structures
- 7ND3 · EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-40 Fab · 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 7ND3 · PDBe 7ND3 · UniProt P0DTC2
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