MolNFT v1 · #186171 · protein
Structure of the SARS-cov-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment
7R40: “Structure of the SARS-cov-2 spike glycoprotein in complex with the 87G7 antibody Fab fragment”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.82). MolNFT v1 #186171 on GenesisL1: 3D structure, binding sites…
- PDB
- 7R40
- Type
- protein
- Length
- 3,840 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; 87G7 light chain variable region; 87G7 heavy chain variable region
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.82
Structure
electron microscopy · 3 distinct chains · 16% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1053 | 18% helix, 31% strand | P0DTC2 |
| L, F, G | 87G7 light chain variable region | protein | 107 | 3% helix, 25% strand | — |
| H, D, E | 87G7 heavy chain variable region | protein | 120 | 3% helix, 24% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 51 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 | 994 | 0.82 | 0.84 | 122 | empty |
| 2 | 183 | 0.80 | 0.95 | 34 | empty |
| 3 | 942 | 0.79 | 0.81 | 86 | empty |
| 4 | 318 | 0.77 | 0.88 | 43 | empty |
| 5 | 316 | 0.77 | 0.88 | 39 | empty |
Interfaces
12 interfaces between chains.
- A–B · 4453 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 4450 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 4440 Ų buried · 36 hydrogen bonds · protein-protein
- L–H · 858 Ų buried · 4 hydrogen bonds · protein-protein
- G–E · 854 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 42 glycan (disulfide, N-glycosylation, glycosylation).
Compared structures
- 7R40 · Structure of the SARS-CoV-2 spike glycoprotein in complex with the 87G7 antibody 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 7R40 · PDBe 7R40 · UniProt P0DTC2
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