MolNFT v1 · #180605 · protein
Cryo-EM structure of the SARS-cov-2 spike glycoprotein bound to Fab 2- 15
7L57: “Cryo-EM structure of the SARS-cov-2 spike glycoprotein bound to Fab 2- 15”. Electron microscopy, 3 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.78). MolNFT v1 #180605 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 7L57
- Type
- protein
- Length
- 3,192 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab 2-15 variable domain heavy chain; Fab 2-15 variable domain light…
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 983 | 23% helix, 31% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 979 | 22% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 994 | 22% helix, 32% strand | P0DTC2 |
| H | Fab 2-15 variable domain heavy chain | protein | 126 | 5% helix, 38% strand | — |
| L | Fab 2-15 variable domain light chain | protein | 110 | 0% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 copies · chains A, B, C
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-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 | 523 | 0.78 | 0.85 | 84 | empty |
| 2 | 1007 | 0.77 | 0.79 | 121 | empty |
| 3 | 1047 | 0.76 | 0.79 | 117 | empty |
| 4 | 1119 | 0.76 | 0.78 | 108 | empty |
| 5 | 548 | 0.75 | 0.83 | 86 | empty |
Interfaces
6 interfaces between chains.
- A–B · 1343 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 1338 Ų buried · 13 hydrogen bonds · protein-protein
- B–C · 1307 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 141 Ų buried · 0 hydrogen bonds · protein-protein
- B–H · 105 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide, 40 glycan (disulfide, N-glycosylation).
Compared structures
- 7L57 · Cryo-EM structure of the SARS-CoV-2 spike glycoprotein bound to Fab 2-15 · 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 7L57 · PDBe 7L57 · UniProt P0DTC2
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