MolNFT v1 · #182547 · protein
Structure of the SARS-cov-2 spike trimer with one rbd down in complex with the Fab fragment of human neutralizing antibody clone 6
7MW4 · Spike glycoprotein: “Structure of the SARS-cov-2 spike trimer with one rbd down in complex with the Fab fragment of human…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #182547 on GenesisL1…
- PDB
- 7MW4
- Type
- protein
- Length
- 4,290 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab of antibody clone 6, light chain; Fab of antibody clone 6, heavy…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 4 distinct chains · 20% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike glycoprotein | protein | 1001 | 22% helix, 32% strand | P0DTC2 |
| L, E, G | Fab of antibody clone 6, light chain | protein | 215 | 6% helix, 51% strand | — |
| H, D, F | Fab of antibody clone 6, heavy chain | protein | 212 | 5% helix, 56% strand | — |
| A, B | Spike glycoprotein | protein | 1004 | 23% helix, 32% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 74 copies · chains C, A, B
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 | 964 | 0.88 | 0.90 | 119 | empty |
| 2 | 1122 | 0.86 | 0.87 | 132 | empty |
| 3 | 906 | 0.81 | 0.83 | 84 | empty |
| 4 | 587 | 0.80 | 0.86 | 50 | empty |
| 5 | 314 | 0.74 | 0.86 | 39 | empty |
Interfaces
15 interfaces between chains.
- A–B · 4499 Ų buried · 39 hydrogen bonds · protein-protein
- C–A · 4298 Ų buried · 42 hydrogen bonds · protein-protein
- C–B · 4177 Ų buried · 38 hydrogen bonds · protein-protein
- E–D · 1780 Ų buried · 8 hydrogen bonds · protein-protein
- G–F · 1696 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 51 glycan (disulfide, N-glycosylation).
Compared structures
- 7MW4 · Structure of the SARS-CoV-2 Spike trimer with one RBD down in complex with the Fab… · the same entry in another collection · chain C against C, 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 7MW4 · PDBe 7MW4 · UniProt P0DTC2
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