MolNFT v1 · #190327 · protein
SARS-cov-2 spike in complex with Fab of M31A7
7WUH · Spike glycoprotein: “SARS-cov-2 spike in complex with Fab of M31A7”. Electron microscopy, 4 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.85). MolNFT v1 #190327 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7WUH
- Type
- protein
- Length
- 4,431 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; M31A7 Fab heavy chain; M31A7 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN, FUC
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 5 distinct chains · 18% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1038 | 20% helix, 19% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1038 | 20% helix, 19% strand | P0DTC2 |
| E | Spike glycoprotein | protein | 1044 | 20% helix, 17% strand | P0DTC2 |
| D, H, K | M31A7 Fab heavy chain | protein | 218 | 1% helix, 15% strand | — |
| F, I, L | M31A7 Fab light chain | protein | 219 | 8% helix, 25% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 67 copies · chains A, C, E, H, I, K, L
- BMA · beta-D-mannopyranose · sugar · 13 copies · chains E, I
- MAN · alpha-D-mannopyranose · sugar · 13 copies · chains E
- FUC · alpha-L-fucopyranose · sugar · 5 copies · chains A, E
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 | 834 | 0.85 | 0.87 | 113 | empty |
| 2 | 900 | 0.84 | 0.86 | 103 | empty |
| 3 | 694 | 0.83 | 0.87 | 77 | empty |
| 4 | 529 | 0.82 | 0.88 | 93 | empty |
| 5 | 564 | 0.81 | 0.86 | 63 | empty |
Interfaces
16 interfaces between chains.
- A–E · 4507 Ų buried · 51 hydrogen bonds · protein-protein
- A–C · 4337 Ų buried · 57 hydrogen bonds · protein-protein
- C–E · 4141 Ų buried · 53 hydrogen bonds · protein-protein
- D–F · 2167 Ų buried · 17 hydrogen bonds · protein-protein
- K–L · 2140 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 45 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7WUH · SARS-CoV-2 Spike in complex with Fab of m31A7 · 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 7WUH · PDBe 7WUH · UniProt P0DTC2
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