Research workbench
SARS-cov-2 spike ectodomain with Fab FI3A
Analyse SARS-cov-2 spike ectodomain with Fab FI3A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7Q0A
- Type
- protein
- Length
- 3,193 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike GLYCOPROTEIN,SPIKE ECTODOMAIN,SPIKE protein S2'; FI3A Fab heavy chain; FI3A Fab…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 5 distinct chains · 22% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike GLYCOPROTEIN,SPIKE ECTODOMAIN,SPIKE protein S2' | protein | 995 | 24% helix, 31% strand | P0DTC2 |
| B | Spike GLYCOPROTEIN,SPIKE ECTODOMAIN,SPIKE protein S2' | protein | 984 | 24% helix, 30% strand | P0DTC2 |
| C | Spike GLYCOPROTEIN,SPIKE ECTODOMAIN,SPIKE protein S2' | protein | 991 | 24% helix, 32% strand | P0DTC2 |
| Y | FI3A Fab heavy chain | protein | 116 | 5% helix, 49% strand | — |
| Z | FI3A Fab light chain | protein | 107 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 49 copies · chains A, C, B
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 | 891 | 0.87 | 0.89 | 97 | empty |
| 2 | 1139 | 0.85 | 0.85 | 133 | empty |
| 3 | 442 | 0.81 | 0.89 | 62 | empty |
| 4 | 503 | 0.77 | 0.85 | 40 | empty |
| 5 | 394 | 0.76 | 0.86 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–C · 5283 Ų buried · 42 hydrogen bonds · protein-protein
- A–B · 4856 Ų buried · 41 hydrogen bonds · protein-protein
- B–C · 4393 Ų buried · 40 hydrogen bonds · protein-protein
- B–Y · 759 Ų buried · 19 hydrogen bonds · protein-protein
- Y–Z · 756 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 41 disulfide, 38 glycan (disulfide, N-glycosylation).
Compared structures
- 7Q0A · SARS-CoV-2 Spike ectodomain with Fab FI3A · 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 7Q0A · PDBe 7Q0A · UniProt P0DTC2
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