Research workbench
SARS-cov-2 spike protein and P17 Fab complex with one rbd in close state
Analyse SARS-cov-2 spike protein and P17 Fab complex with one rbd in close state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7CWL
- Type
- protein
- Length
- 3,900 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab P17 heavy chain; Fab P17 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 6 distinct chains · 19% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1073 | 21% helix, 29% strand | P0DTC2 |
| B | Spike glycoprotein | protein | 1070 | 22% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1074 | 21% helix, 30% strand | P0DTC2 |
| G, H, I | Fab P17 heavy chain | protein | 120 | 5% helix, 45% strand | — |
| L, J | Fab P17 light chain | protein | 108 | 0% helix, 54% strand | — |
| K | Fab P17 light chain | protein | 107 | 0% helix, 54% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 27 copies · chains A, B, C
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 | 881 | 0.89 | 0.91 | 121 | empty |
| 2 | 882 | 0.84 | 0.86 | 91 | empty |
| 3 | 1177 | 0.82 | 0.83 | 108 | empty |
| 4 | 517 | 0.74 | 0.82 | 36 | empty |
| 5 | 558 | 0.73 | 0.81 | 41 | empty |
Interfaces
13 interfaces between chains.
- A–B · 4369 Ų buried · 36 hydrogen bonds · protein-protein
- B–C · 4354 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 4322 Ų buried · 32 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: 45 disulfide, 27 glycan (disulfide, N-glycosylation).
Compared structures
- 7CWL · SARS-CoV-2 spike protein and P17 fab complex with one RBD in close state · 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 7CWL · PDBe 7CWL · UniProt P0DTC2
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