Research workbench
SARS-cov-2 spike proteins trimer in complex with P17 and FC05 fabs cocktail
Analyse SARS-cov-2 spike proteins trimer in complex with P17 and FC05 fabs cocktail in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CWU
- Type
- protein
- Length
- 4,592 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; Spike glycoprotein; Heavy chain of P17…
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.88
Structure
electron microscopy · 7 distinct chains · 19% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| P, N, J | Heavy chain of FC05 Fab | protein | 120 | 3% helix, 29% strand | — |
| I, G, F | Light chain of FC05 Fab | protein | 109 | 5% helix, 44% strand | — |
| B | Spike glycoprotein | protein | 1076 | 21% helix, 29% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1070 | 21% helix, 30% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 1075 | 22% helix, 30% strand | P0DTC2 |
| H, M, O | Heavy chain of P17 Fab | protein | 120 | 5% helix, 45% strand | — |
| L, R, S | Light chain of P17 Fab | protein | 108 | 0% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 46 copies · chains B, C, A
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.
- B–C · 4118 Ų buried · 33 hydrogen bonds · protein-protein
- C–A · 4095 Ų buried · 38 hydrogen bonds · protein-protein
- B–A · 4095 Ų buried · 40 hydrogen bonds · protein-protein
- P–I · 947 Ų buried · 4 hydrogen bonds · protein-protein
- J–F · 932 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide, 30 glycan (disulfide, N-glycosylation).
Compared structures
- 7CWU · SARS-CoV-2 spike proteins trimer in complex with P17 and FC05 Fabs cocktail · the same entry in another collection · chain P against P, 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 7CWU · PDBe 7CWU · UniProt P0DTC2
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