Research workbench
SARS-cov-2 spike proteins trimer in complex with FC05 and H014 fabs cocktail
Analyse SARS-cov-2 spike proteins trimer in complex with FC05 and H014 fabs cocktail in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CWS
- Type
- protein
- Length
- 4,602 residues
- Chains
- 15
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of FC05 Fab; Light chain of FC05 Fab; Light chain of H014 Fab; Heavy chain of…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 5 distinct chains · 15% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, N, P | Heavy chain of FC05 Fab | protein | 120 | 3% helix, 29% strand | — |
| C, K, M | Light chain of FC05 Fab | protein | 109 | 5% helix, 44% strand | — |
| D, F, H | Light chain of H014 Fab | protein | 107 | 0% helix, 44% strand | — |
| E, G, I | Heavy chain of H014 Fab | protein | 122 | 0% helix, 43% strand | — |
| O, Q, R | Spike glycoprotein | protein | 1076 | 20% helix, 29% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 46 copies · chains O, Q, R
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 | 698 | 0.88 | 0.92 | 99 | empty |
| 2 | 638 | 0.81 | 0.86 | 68 | empty |
| 3 | 385 | 0.75 | 0.85 | 48 | empty |
| 4 | 519 | 0.74 | 0.82 | 39 | empty |
| 5 | 574 | 0.73 | 0.81 | 42 | empty |
Interfaces
21 interfaces between chains.
- O–Q · 4228 Ų buried · 37 hydrogen bonds · protein-protein
- Q–R · 4196 Ų buried · 41 hydrogen bonds · protein-protein
- O–R · 4184 Ų buried · 41 hydrogen bonds · protein-protein
- L–C · 947 Ų buried · 4 hydrogen bonds · protein-protein
- P–M · 932 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 48 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 7CWS · SARS-CoV-2 Spike Proteins Trimer in Complex with FC05 and H014 Fabs Cocktail · the same entry in another collection · chain L against L, 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 7CWS · PDBe 7CWS · UniProt P0DTC2
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