MolNFT v1 · #179125 · protein
SARS-cov-2 spike in complex with the S304 neutralizing antibody Fab fragment
7JW0 · Spike glycoprotein: “SARS-cov-2 spike in complex with the S304 neutralizing antibody Fab fragment”. Electron microscopy, 2 ligands (NAG, BMA), 20 pockets (best druggability 0.86). MolNFT v1 #179125 on GenesisL1: 3D structure…
- PDB
- 7JW0
- Type
- protein
- Length
- 4,314 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; S304 Fab light chain; S304 Fab heavy chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 18% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Spike glycoprotein | protein | 1007 | 22% helix, 33% strand | P0DTC2 |
| L, C, F | S304 Fab light chain | protein | 212 | 5% helix, 52% strand | — |
| H, D, G | S304 Fab heavy chain | protein | 219 | 10% helix, 56% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 66 copies · chains A, B, E
- BMA · beta-D-mannopyranose · sugar · 3 copies
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 | 870 | 0.86 | 0.88 | 130 | empty |
| 2 | 664 | 0.85 | 0.88 | 79 | empty |
| 3 | 1098 | 0.82 | 0.84 | 126 | empty |
| 4 | 1121 | 0.82 | 0.84 | 123 | empty |
| 5 | 1119 | 0.82 | 0.84 | 123 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2711 Ų buried · 17 hydrogen bonds · protein-protein
- A–E · 2710 Ų buried · 17 hydrogen bonds · protein-protein
- B–E · 2708 Ų buried · 17 hydrogen bonds · protein-protein
- F–G · 766 Ų buried · 1 hydrogen bond · protein-protein
- C–D · 765 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 51 disulfide, 51 glycan (disulfide, N-glycosylation).
Compared structures
- 7JW0 · SARS-CoV-2 spike in complex with the S304 neutralizing antibody Fab fragment · 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 7JW0 · PDBe 7JW0 · UniProt P0DTC2
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