MolNFT v1 · #183043 · protein
EM structure of SARS-cov-2 spike glycoprotein in complex with covox-88 Fab
7ND4: “EM structure of SARS-cov-2 spike glycoprotein in complex with covox-88 Fab”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.86). MolNFT v1 #183043 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7ND4
- Type
- protein
- Length
- 3,729 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Covox-88 Fab heavy chain; Covox-88 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 19% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1002 | 22% helix, 32% strand | P0DTC2 |
| H, D, F | Covox-88 Fab heavy chain | protein | 128 | 5% helix, 49% strand | — |
| L, E, G | Covox-88 Fab light chain | protein | 113 | 3% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 66 copies · chains A, B, C, H, D, F
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains C, A, B
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains 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 | 566 | 0.86 | 0.91 | 91 | empty |
| 2 | 817 | 0.85 | 0.87 | 102 | empty |
| 3 | 551 | 0.77 | 0.84 | 44 | empty |
| 4 | 425 | 0.76 | 0.86 | 43 | empty |
| 5 | 497 | 0.75 | 0.83 | 42 | empty |
Interfaces
12 interfaces between chains.
- B–C · 4398 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 4392 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 4369 Ų buried · 36 hydrogen bonds · protein-protein
- H–L · 847 Ų buried · 9 hydrogen bonds · protein-protein
- F–G · 845 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 48 glycan (disulfide, N-glycosylation).
Compared structures
- 7ND4 · EM structure of SARS-CoV-2 Spike glycoprotein in complex with COVOX-88 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 7ND4 · PDBe 7ND4 · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.