Research workbench
SARS-cov-2 spike protein in complex with HB27 and FC05 Fab cocktail
Analyse SARS-cov-2 spike protein in complex with HB27 and FC05 Fab cocktail in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CWT
- Type
- protein
- Length
- 4,584 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Light chain Fab of HB27; Heavy chain Fab of HB27; Light chain Fab of…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 7 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1065 | 21% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1071 | 21% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1074 | 22% helix, 30% strand | P0DTC2 |
| D, F, J | Light chain Fab of HB27 | protein | 111 | 0% helix, 41% strand | — |
| E, G, I | Heavy chain Fab of HB27 | protein | 118 | 3% helix, 42% strand | — |
| H, K, M | Light chain Fab of FC05 | protein | 109 | 7% helix, 44% strand | — |
| L, N, P | Heavy chain Fab of FC05 | protein | 120 | 3% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 14 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 | 903 | 0.89 | 0.91 | 128 | empty |
| 2 | 506 | 0.79 | 0.86 | 50 | empty |
| 3 | 466 | 0.76 | 0.84 | 37 | empty |
| 4 | 346 | 0.74 | 0.86 | 41 | empty |
| 5 | 531 | 0.73 | 0.81 | 37 | empty |
Interfaces
23 interfaces between chains.
- B–C · 4563 Ų buried · 35 hydrogen bonds · protein-protein
- A–C · 4423 Ų buried · 39 hydrogen bonds · protein-protein
- A–B · 4314 Ų buried · 35 hydrogen bonds · protein-protein
- K–N · 918 Ų buried · 6 hydrogen bonds · protein-protein
- H–L · 916 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 18 glycan (disulfide, N-glycosylation, O-glycosylation).
Compared structures
- 7CWT · SARS-CoV-2 Spike protein in complex with hb27 and fc05 Fab cocktail · 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 7CWT · PDBe 7CWT · UniProt P0DTC2
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