MolNFT v1 · #176968 · protein
SARS-cov-2 spike in complex with the AB1 neutralizing antibody (focused refinement on Fab-rbd)
7E3C · Spike protein S1: “SARS-cov-2 spike in complex with the AB1 neutralizing antibody (focused refinement on Fab-rbd)”. Electron microscopy, 1 ligand (NAG), 5 pockets (best druggability 0.69). MolNFT v1 #176968 on GenesisL1: 3D…
- PDB
- 7E3C
- Type
- protein
- Length
- 405 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike protein S1; Light chain of AB1; Heavy chain of AB1
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.69
Structure
electron microscopy · 3 distinct chains · 6% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 11% helix, 26% strand | P0DTC2 |
| C | Light chain of AB1 | protein | 102 | 0% helix, 37% strand | — |
| B | Heavy chain of AB1 | protein | 109 | 3% helix, 40% 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 151 | 0.69 | 0.89 | 32 | empty |
| 2 | 93 | 0.64 | 0.90 | 29 | empty |
| 3 | 81 | 0.59 | 0.88 | 24 | empty |
| 4 | 140 | 0.59 | 0.84 | 42 | empty |
| 5 | 61 | 0.30 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–B · 801 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 750 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 495 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7E3C · SARS-CoV-2 spike in complex with the Ab1 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 7E3C · PDBe 7E3C · UniProt P0DTC2
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