Research workbench
Cryo-EM structure of SARS-cov-2 spike in complex with a neutralizing antibody chab-45 (focused refinement of S-rbd and chab-45 region)
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
- 7F63
- Type
- protein
- Length
- 429 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Rbd-CHAB45, heavy chain; Rbd-CHAB45, light chain
- UniProt
- P0DTC2
- Pockets
- 6 · best druggability 0.72
Structure
electron microscopy · 3 distinct chains · 6% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 199 | 13% helix, 23% strand | P0DTC2 |
| H | Rbd-CHAB45, heavy chain | protein | 120 | 0% helix, 46% strand | — |
| L | Rbd-CHAB45, light chain | protein | 110 | 0% helix, 31% strand | — |
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 69 | 0.72 | 0.96 | 22 | empty |
| 2 | 119 | 0.42 | 0.76 | 17 | empty |
| 3 | 77 | 0.40 | 0.78 | 18 | empty |
| 4 | 86 | 0.37 | 0.76 | 18 | empty |
| 5 | 69 | 0.37 | 0.77 | 13 | empty |
Interfaces
3 interfaces between chains.
- H–L · 831 Ų buried · 3 hydrogen bonds · protein-protein
- A–H · 440 Ų buried · 3 hydrogen bonds · protein-protein
- A–L · 216 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 7F63 · Cryo-EM structure of SARS-CoV-2 spike in complex with a neutralizing antibody 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 7F63 · PDBe 7F63 · UniProt P0DTC2
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