Research workbench
Cryo-EM structure of SARS-cov-2 spike in complex with neutralizing antibody B1-182.1 that targets the receptor-binding domain
Analyse Cryo-EM structure of SARS-cov-2 spike in complex with neutralizing antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MM0
- Type
- protein
- Length
- 3,490 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- B1-182.1 Fab heavy chain; B1-182.1 Fab light chain; Spike glycoprotein
- UniProt
- P0DTC2
- Ligands
- NAG, BMA
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 19% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | B1-182.1 Fab heavy chain | protein | 122 | 5% helix, 33% strand | — |
| L | B1-182.1 Fab light chain | protein | 107 | 0% helix, 28% strand | — |
| A | Spike glycoprotein | protein | 1085 | 19% helix, 25% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1088 | 21% helix, 26% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1088 | 19% helix, 23% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 55 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar
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 | 1143 | 0.86 | 0.87 | 115 | empty |
| 2 | 1028 | 0.86 | 0.87 | 115 | empty |
| 3 | 708 | 0.80 | 0.84 | 76 | empty |
| 4 | 1056 | 0.76 | 0.79 | 104 | empty |
| 5 | 675 | 0.76 | 0.81 | 66 | empty |
Interfaces
6 interfaces between chains.
- B–C · 4584 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 4227 Ų buried · 27 hydrogen bonds · protein-protein
- A–C · 3923 Ų buried · 25 hydrogen bonds · protein-protein
- H–L · 822 Ų buried · 1 hydrogen bond · protein-protein
- H–A · 583 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide, 42 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7MM0 · Cryo-EM structure of SARS-CoV-2 spike in complex with neutralizing antibody B1-182.1 that… · the same entry in another collection · chain H against H, 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 7MM0 · PDBe 7MM0 · UniProt P0DTC2
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