Research workbench
SARS-cov-2 spike protein in complex with three human neutralizing antibodies
Analyse SARS-cov-2 spike protein in complex with three human neutralizing antibodies in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7WHZ
- Type
- protein
- Length
- 887 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; XMA04 heavy chain variable domain; XMA01 heavy chain variable domain…
- UniProt
- P0DTC2, A0A5C2G4I7, A0A5C2GTV1, A0A5C2GVU3
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.72
Structure
electron microscopy · 7 distinct chains · 2% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 5% helix, 24% strand | P0DTC2 |
| B | XMA04 heavy chain variable domain | protein | 124 | 0% helix, 38% strand | — |
| C | XMA01 heavy chain variable domain | protein | 122 | 5% helix, 49% strand | — |
| D | Igl C4029_LIGHT_IGKV1-39_IGKJ2 | protein | 107 | 0% helix, 51% strand | A0A5C2G4I7 |
| E | Ig C934_LIGHT_IGKV1-5_IGKJ1 | protein | 107 | 0% helix, 37% strand | A0A5C2GTV1 |
| H | XMA09 heavy chain variable domain | protein | 123 | 0% helix, 35% strand | — |
| L | Ig C1437_LIGHT_IGLV1-40_IGLJ1 | protein | 110 | 0% helix, 37% strand | A0A5C2GVU3 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 738 | 0.72 | 0.79 | 64 | empty |
| 2 | 466 | 0.62 | 0.76 | 46 | empty |
| 3 | 314 | 0.61 | 0.78 | 32 | empty |
| 4 | 134 | 0.44 | 0.77 | 25 | empty |
| 5 | 153 | 0.41 | 0.74 | 32 | empty |
Interfaces
12 interfaces between chains.
- C–E · 919 Ų buried · 7 hydrogen bonds · protein-protein
- H–L · 862 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 807 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 779 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 661 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7WHZ · SARS-CoV-2 spike protein in complex with three human neutralizing antibodies · 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
- Every structure of UniProt A0A5C2G4I7
- Every structure of UniProt A0A5C2GTV1
- Every structure of UniProt A0A5C2GVU3
- Elsewhere: RCSB PDB 7WHZ · PDBe 7WHZ · UniProt P0DTC2 · UniProt A0A5C2G4I7 · UniProt A0A5C2GTV1 · UniProt A0A5C2GVU3
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