MolNFT v1 · #186280 · protein
Structure of the SARS-cov-2 S 6P trimer in complex with neutralizing antibody C032
7R8M · Spike glycoprotein: “Structure of the SARS-cov-2 S 6P trimer in complex with neutralizing antibody C032”. Electron microscopy, 2 ligands (NAG, FUC), 20 pockets (best druggability 0.86). MolNFT v1 #186280 on GenesisL1: 3D structure…
- PDB
- 7R8M
- Type
- protein
- Length
- 3,411 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; C032 Fab heavy chain; C032 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 5 distinct chains · 20% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 968 | 21% helix, 24% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1003 | 21% helix, 25% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 978 | 22% helix, 21% strand | P0DTC2 |
| D, H | C032 Fab heavy chain | protein | 121 | 5% helix, 46% strand | — |
| E, L | C032 Fab light chain | protein | 110 | 3% helix, 42% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains A, B, H, C, D, E
- FUC · alpha-L-fucopyranose · sugar · chains B, H, L
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 | 812 | 0.86 | 0.88 | 104 | empty |
| 2 | 1064 | 0.83 | 0.84 | 135 | empty |
| 3 | 916 | 0.79 | 0.82 | 107 | empty |
| 4 | 811 | 0.75 | 0.79 | 91 | empty |
| 5 | 356 | 0.74 | 0.86 | 52 | empty |
Interfaces
11 interfaces between chains.
- B–C · 5302 Ų buried · 47 hydrogen bonds · protein-protein
- A–C · 4989 Ų buried · 56 hydrogen bonds · protein-protein
- A–B · 4533 Ų buried · 49 hydrogen bonds · protein-protein
- H–L · 911 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 907 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 37 disulfide, 27 glycan (disulfide, N-glycosylation).
Compared structures
- 7R8M · Structure of the SARS-CoV-2 S 6P trimer in complex with neutralizing antibody C032 · 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 7R8M · PDBe 7R8M · UniProt P0DTC2
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