Research workbench
Cryo-EM structure of SARS-cov-2 spike in complex with a neutralizing antibody rbd-chab-45
Analyse Cryo-EM structure of SARS-cov-2 spike in complex with a neutralizing antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EJ5
- Type
- protein
- Length
- 3,723 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Rbd-CHAB45, heavy chain; Rbd-CHAB45, light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 5 distinct chains · 20% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1008 | 22% helix, 28% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1014 | 21% helix, 28% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1011 | 21% helix, 30% strand | P0DTC2 |
| H, I, J | Rbd-CHAB45, heavy chain | protein | 120 | 0% helix, 44% strand | — |
| L, M, N | Rbd-CHAB45, light chain | protein | 110 | 0% helix, 29% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 72 copies · chains A, B, C
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 | 1014 | 0.88 | 0.89 | 96 | empty |
| 2 | 829 | 0.85 | 0.87 | 104 | empty |
| 3 | 329 | 0.77 | 0.88 | 45 | empty |
| 4 | 62 | 0.74 | 0.98 | 17 | empty |
| 5 | 85 | 0.74 | 0.96 | 29 | empty |
Interfaces
12 interfaces between chains.
- A–C · 3925 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 3897 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 3776 Ų buried · 31 hydrogen bonds · protein-protein
- J–N · 873 Ų buried · 3 hydrogen bonds · protein-protein
- H–L · 831 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 43 disulfide (N-glycosylation, disulfide).
Compared structures
- 7EJ5 · Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody RBD-chAb-45 · 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 7EJ5 · PDBe 7EJ5 · UniProt P0DTC2
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