MolNFT v1 · #174916 · protein
SARS-cov-2 S trimer with three rbd in the open state and complexed with three H014 Fab
7CAK · Spike glycoprotein: “SARS-cov-2 S trimer with three rbd in the open state and complexed with three H014 Fab”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.89). MolNFT v1 #174916 on GenesisL1: 3D structure…
- PDB
- 7CAK
- Type
- protein
- Length
- 3,771 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Light chain of H014 Fab; Heavy chain of H014 Fab
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.89
Structure
electron microscopy · 3 distinct chains · 16% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1028 | 20% helix, 24% strand | P0DTC2 |
| 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 | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 60 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 | 864 | 0.89 | 0.91 | 119 | empty |
| 2 | 1056 | 0.86 | 0.87 | 156 | empty |
| 3 | 1148 | 0.78 | 0.80 | 112 | empty |
| 4 | 314 | 0.75 | 0.87 | 45 | empty |
| 5 | 185 | 0.73 | 0.90 | 38 | empty |
Interfaces
12 interfaces between chains.
- A–C · 3870 Ų buried · 31 hydrogen bonds · protein-protein
- B–C · 3848 Ų buried · 30 hydrogen bonds · protein-protein
- A–B · 3838 Ų buried · 28 hydrogen bonds · protein-protein
- H–I · 816 Ų buried · 7 hydrogen bonds · protein-protein
- D–E · 812 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 glycan, 39 disulfide (N-glycosylation, disulfide).
Compared structures
- 7CAK · SARS-CoV-2 S trimer with three RBD in the open state and complexed with three H014 Fab · 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 7CAK · PDBe 7CAK · UniProt P0DTC2
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