MolNFT v1 · #182549 · protein
Structure of the SARS-cov-2 spike trimer with three rbds up in complex with the Fab fragment of human neutralizing antibody clone 2
7MW6 · Spike glycoprotein: “Structure of the SARS-cov-2 spike trimer with three rbds up in complex with the Fab fragment of human…”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.88). MolNFT v1 #182549 on GenesisL1…
- PDB
- 7MW6
- Type
- protein
- Length
- 4,446 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab of antibody clone 2, light chain; Fab of antibody clone 2, heavy…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 3 distinct chains · 16% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, B | Spike glycoprotein | protein | 1058 | 21% helix, 31% strand | P0DTC2 |
| E, L, G | Fab of antibody clone 2, light chain | protein | 215 | 5% helix, 42% strand | — |
| D, H, F | Fab of antibody clone 2, heavy chain | protein | 209 | 3% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 87 copies · chains A, B, 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 | 966 | 0.88 | 0.89 | 101 | empty |
| 2 | 955 | 0.84 | 0.86 | 114 | empty |
| 3 | 393 | 0.76 | 0.86 | 64 | empty |
| 4 | 563 | 0.75 | 0.82 | 46 | empty |
| 5 | 708 | 0.75 | 0.81 | 54 | empty |
Interfaces
12 interfaces between chains.
- C–B · 4248 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 4242 Ų buried · 43 hydrogen bonds · protein-protein
- A–C · 4228 Ų buried · 41 hydrogen bonds · protein-protein
- E–D · 1654 Ų buried · 9 hydrogen bonds · protein-protein
- L–H · 1612 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 54 glycan, 51 disulfide (N-glycosylation, disulfide).
Compared structures
- 7MW6 · Structure of the SARS-CoV-2 Spike trimer with three RBDs up in complex with the Fab… · 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 7MW6 · PDBe 7MW6 · UniProt P0DTC2
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