Research workbench
Structure of the SARS-cov-2 S 2P trimer in complex with the human neutralizing antibody Fab fragment, BG1-24
Analyse Structure of the SARS-cov-2 S 2P trimer in complex with the human neutralizing… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7M6I
- Type
- protein
- Length
- 3,450 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; BG1-24 Fab heavy chain; BG1-24 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 21% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1002 | 22% helix, 29% strand | P0DTC2 |
| B, C | Spike glycoprotein | protein | 1001 | 22% helix, 29% strand | P0DTC2 |
| H, M | BG1-24 Fab heavy chain | protein | 117 | 5% helix, 33% strand | — |
| L, N | BG1-24 Fab light chain | protein | 106 | 3% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 36 copies · chains A, C, B
- BMA · beta-D-mannopyranose · sugar · 2 copies
- MAN · alpha-D-mannopyranose · sugar · chains H
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 | 744 | 0.83 | 0.86 | 64 | empty |
| 2 | 983 | 0.82 | 0.83 | 96 | empty |
| 3 | 574 | 0.81 | 0.87 | 75 | empty |
| 4 | 275 | 0.79 | 0.91 | 49 | empty |
| 5 | 805 | 0.78 | 0.81 | 91 | empty |
Interfaces
11 interfaces between chains.
- A–C · 5210 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 4810 Ų buried · 36 hydrogen bonds · protein-protein
- A–B · 4593 Ų buried · 35 hydrogen bonds · protein-protein
- M–N · 892 Ų buried · 11 hydrogen bonds · protein-protein
- H–L · 857 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 29 glycan (disulfide, N-glycosylation).
Compared structures
- 7M6I · Structure of the SARS-CoV-2 S 2P 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 7M6I · PDBe 7M6I · UniProt P0DTC2
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.