Research workbench
Complex of SARS-cov-2 spike protein and Fab P17 with one rbd in open state and two rbd in closed state
Analyse Complex of SARS-cov-2 spike protein and Fab P17 with one rbd in open state and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CWM
- Type
- protein
- Length
- 3,883 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; P17 heavy chain; P17 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 5 distinct chains · 20% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1056 | 22% helix, 30% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1071 | 21% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1072 | 21% helix, 30% strand | P0DTC2 |
| G, H, I | P17 heavy chain | protein | 120 | 5% helix, 45% strand | — |
| L, J, K | P17 light chain | protein | 108 | 0% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 44 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 | 972 | 0.89 | 0.91 | 138 | empty |
| 2 | 1044 | 0.79 | 0.81 | 84 | empty |
| 3 | 860 | 0.77 | 0.80 | 68 | empty |
| 4 | 273 | 0.73 | 0.87 | 42 | empty |
| 5 | 551 | 0.73 | 0.81 | 41 | empty |
Interfaces
13 interfaces between chains.
- A–C · 4802 Ų buried · 43 hydrogen bonds · protein-protein
- A–B · 4572 Ų buried · 46 hydrogen bonds · protein-protein
- B–C · 4428 Ų buried · 34 hydrogen bonds · protein-protein
- G–J · 874 Ų buried · 8 hydrogen bonds · protein-protein
- H–L · 873 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 43 disulfide, 29 glycan (disulfide, N-glycosylation).
Compared structures
- 7CWM · Complex of SARS-CoV-2 spike protein and Fab P17 with one RBD in open state and two RBD in… · 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 7CWM · PDBe 7CWM · UniProt P0DTC2
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