MolNFT v1 · #190228 · protein
SARS-cov-2 spike in complex with IgG 553-60 (1-up trimer)
7WOA · Spike glycoprotein: “SARS-cov-2 spike in complex with IgG 553-60 (1-up trimer)”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.81). MolNFT v1 #190228 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7WOA
- Type
- protein
- Length
- 4,060 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; MAB60 vh; MAB60 vl
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · 3 distinct chains · 14% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Spike glycoprotein | protein | 1076 | 19% helix, 27% strand | P0DTC2 |
| D, F | MAB60 vh | protein | 204 | 1% helix, 40% strand | — |
| B, G | MAB60 vl | protein | 212 | 3% helix, 35% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, E, C
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 | 835 | 0.81 | 0.84 | 68 | empty |
| 2 | 1023 | 0.81 | 0.82 | 93 | empty |
| 3 | 807 | 0.81 | 0.84 | 86 | empty |
| 4 | 539 | 0.80 | 0.87 | 59 | empty |
| 5 | 585 | 0.80 | 0.85 | 65 | empty |
Interfaces
11 interfaces between chains.
- A–E · 4696 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 4654 Ų buried · 42 hydrogen bonds · protein-protein
- C–E · 4260 Ų buried · 33 hydrogen bonds · protein-protein
- F–G · 1742 Ų buried · 17 hydrogen bonds · protein-protein
- D–B · 1673 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 disulfide, 39 glycan (disulfide, N-glycosylation).
Compared structures
- 7WOA · SARS-CoV-2 Spike in complex with IgG 553-60 (1-up trimer) · 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 7WOA · PDBe 7WOA · UniProt P0DTC2
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