MolNFT v1 · #181799 · protein
Structure of the SARS-cov-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG1-22
7M6F · Spike glycoprotein: “Structure of the SARS-cov-2 S 6P trimer in complex with the human neutralizing antibody Fab fragment, BG1-22”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.87). MolNFT v1 #181799 on…
- PDB
- 7M6F
- Type
- protein
- Length
- 3,446 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; BG1-22 Fab heavy chain; BG1-22 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E | Spike glycoprotein | protein | 998 | 22% helix, 35% strand | P0DTC2 |
| C, H | BG1-22 Fab heavy chain | protein | 118 | 0% helix, 41% strand | — |
| D, L | BG1-22 Fab light chain | protein | 108 | 0% helix, 35% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 63 copies · chains A, E, 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 | 1169 | 0.87 | 0.88 | 163 | empty |
| 2 | 1010 | 0.83 | 0.84 | 125 | empty |
| 3 | 513 | 0.80 | 0.87 | 108 | empty |
| 4 | 332 | 0.77 | 0.88 | 65 | empty |
| 5 | 391 | 0.76 | 0.87 | 71 | empty |
Interfaces
9 interfaces between chains.
- A–B · 4023 Ų buried · 28 hydrogen bonds · protein-protein
- A–E · 3993 Ų buried · 29 hydrogen bonds · protein-protein
- B–E · 3932 Ų buried · 34 hydrogen bonds · protein-protein
- A–H · 423 Ų buried · 4 hydrogen bonds · protein-protein
- H–L · 404 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 glycan, 41 disulfide (N-glycosylation, disulfide).
Compared structures
- 7M6F · Structure of the SARS-CoV-2 S 6P trimer in complex with the human neutralizing antibody… · 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 7M6F · PDBe 7M6F · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.