Research workbench
Cryo-EM structure of SARS-cov-2 gamma (P.1) spike protein in complex with Fab 4A8 (focused refinement of ntd and 4A8)
Analyse Cryo-EM structure of SARS-cov-2 gamma (P.1) spike protein in complex with Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DLS
- Type
- protein
- Length
- 495 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab 4A8 heavy chain; Fab 4A8 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.49
Structure
electron microscopy · 3 distinct chains · 2% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 255 | 0% helix, 53% strand | P0DTC2 |
| H | Fab 4A8 heavy chain | protein | 128 | 5% helix, 50% strand | — |
| L | Fab 4A8 light chain | protein | 112 | 3% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 65 | 0.49 | 0.85 | 18 | empty |
| 2 | 50 | 0.45 | 0.85 | 12 | empty |
| 3 | 80 | 0.37 | 0.77 | 18 | empty |
| 4 | 71 | 0.31 | 0.74 | 18 | empty |
| 5 | 58 | 0.27 | 0.73 | 13 | empty |
Interfaces
3 interfaces between chains.
- H–L · 945 Ų buried · 1 hydrogen bond · protein-protein
- A–H · 862 Ų buried · 14 hydrogen bonds · protein-protein
- A–L · 35 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 4 disulfide (N-glycosylation, disulfide).
Compared structures
- 8DLS · Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4A8… · 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 8DLS · PDBe 8DLS · UniProt P0DTC2
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