Research workbench
Three rbd-down state of SARS-cov-2 D614G spike in complex with the SP1-77 neutralizing antibody Fab fragment (local refinement of the rbd and Fab variable domains)
Analyse Three rbd-down state of SARS-cov-2 D614G spike in complex with the SP1-77… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7UPX
- Type
- protein
- Length
- 635 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; SP1-77 Fab heavy chain; SP1-77 Fab light chain
- UniProt
- P0DTC2
- Ligands
- NAG, FUC
- Pockets
- 7 · best druggability 0.62
Structure
electron microscopy · 3 distinct chains · 9% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 198 | 16% helix, 27% strand | P0DTC2 |
| H | SP1-77 Fab heavy chain | protein | 225 | 8% helix, 48% strand | — |
| L | SP1-77 Fab light chain | protein | 212 | 5% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A, H
- FUC · alpha-L-fucopyranose · sugar · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.62 | 0.77 | 34 | empty |
| 2 | 267 | 0.51 | 0.75 | 43 | empty |
| 3 | 131 | 0.48 | 0.79 | 24 | empty |
| 4 | 109 | 0.41 | 0.76 | 18 | empty |
| 5 | 66 | 0.39 | 0.79 | 15 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1940 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 568 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 148 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7UPX · Three RBD-down state of SARS-CoV-2 D614G spike in complex with the SP1-77 neutralizing… · 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 7UPX · PDBe 7UPX · UniProt P0DTC2
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