Research workbench
SARS-cov-2 spike in complex with the S2H13 neutralizing antibody (closed conformation)
Analyse SARS-cov-2 spike in complex with the S2H13 neutralizing antibody (closed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7JV6
- Type
- protein
- Length
- 3,612 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; S2H13 Fab heavy chain; S2H13 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 3 distinct chains · 19% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Spike glycoprotein | protein | 977 | 22% helix, 34% strand | P0DTC2 |
| H, C, F | S2H13 Fab heavy chain | protein | 118 | 3% helix, 49% strand | — |
| L, D, G | S2H13 Fab light chain | protein | 109 | 6% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 copies · chains A, B, E
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 | 1078 | 0.85 | 0.86 | 156 | empty |
| 2 | 1113 | 0.85 | 0.86 | 157 | empty |
| 3 | 1014 | 0.84 | 0.85 | 121 | empty |
| 4 | 1189 | 0.83 | 0.84 | 118 | empty |
| 5 | 211 | 0.81 | 0.94 | 35 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4838 Ų buried · 37 hydrogen bonds · protein-protein
- A–E · 4834 Ų buried · 37 hydrogen bonds · protein-protein
- B–E · 4825 Ų buried · 37 hydrogen bonds · protein-protein
- F–G · 456 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 453 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7JV6 · SARS-CoV-2 spike in complex with the S2H13 neutralizing antibody (closed conformation) · 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 7JV6 · PDBe 7JV6 · UniProt P0DTC2
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