MolNFT v1 · #176967 · protein
SARS-cov-2 spike in complex with the AB5 neutralizing antibody (focused refinement on Fab-rbd)
7E3B · Spike protein S1: “SARS-cov-2 spike in complex with the AB5 neutralizing antibody (focused refinement on Fab-rbd)”. Electron microscopy, 1 ligand (NAG), 5 pockets (best druggability 0.44). MolNFT v1 #176967 on GenesisL1: 3D…
- PDB
- 7E3B
- Type
- protein
- Length
- 421 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Heavy chain of AB5; Light chain of AB5
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.44
Structure
electron microscopy · 3 distinct chains · 8% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 15% helix, 26% strand | P0DTC2 |
| B | Heavy chain of AB5 | protein | 122 | 5% helix, 47% strand | — |
| C | Light chain of AB5 | protein | 105 | 0% helix, 42% strand | — |
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
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 98 | 0.44 | 0.79 | 16 | empty |
| 2 | 79 | 0.37 | 0.77 | 19 | empty |
| 3 | 69 | 0.34 | 0.76 | 21 | empty |
| 4 | 68 | 0.33 | 0.76 | 16 | empty |
| 5 | 69 | 0.29 | 0.74 | 17 | empty |
Interfaces
3 interfaces between chains.
- A–B · 921 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 845 Ų buried · 1 hydrogen bond · protein-protein
- A–C · 201 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7E3B · SARS-Cov-2 spike in complex with the Ab5 neutralizing antibody (focused refinement on… · 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 7E3B · PDBe 7E3B · UniProt P0DTC2
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