Research workbench
Cryo-EM structure of SARS-cov-2 gamma (P.1) spike protein in complex with Fab 4-8 (focused refinement of ntd and 4-8)
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
- 8DLR
- Type
- protein
- Length
- 505 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab 4-8 heavy chain; Fab 4-8 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 3 · best druggability 0.34
Structure
electron microscopy · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 274 | 4% helix, 53% strand | P0DTC2 |
| H | Fab 4-8 heavy chain | protein | 125 | 8% helix, 46% strand | — |
| L | Fab 4-8 light chain | protein | 106 | 6% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.34 | 0.75 | 15 | empty |
| 2 | 53 | 0.33 | 0.77 | 16 | empty |
| 3 | 53 | 0.26 | 0.73 | 12 | empty |
Interfaces
3 interfaces between chains.
- H–L · 805 Ų buried · 11 hydrogen bonds · protein-protein
- A–H · 675 Ų buried · 9 hydrogen bonds · protein-protein
- A–L · 395 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 glycan, 5 disulfide (N-glycosylation, disulfide).
Compared structures
- 8DLR · Cryo-EM structure of SARS-CoV-2 Gamma (P.1) spike protein in complex with Fab 4-8… · the same entry in another collection · chain H against H, 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 8DLR · PDBe 8DLR · UniProt P0DTC2
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