MolNFT v1 · #176857 · protein
Spike protein from SARS-COV2 with Fab fragment of enhancing antibody 8D2
7DZX · Spike glycoprotein: “Spike protein from SARS-COV2 with Fab fragment of enhancing antibody 8D2”. Electron microscopy, 20 pockets (best druggability 0.73). MolNFT v1 #176857 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 7DZX
- Type
- protein
- Length
- 3,803 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Fab heavy chain of enhancing antibody; Fab light chain of enhancing…
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.73
Structure
electron microscopy · 3 distinct chains · 18% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 1121 | 23% helix, 30% strand | P0DTC2 |
| H | Fab heavy chain of enhancing antibody | protein | 227 | 5% helix, 44% strand | — |
| L | Fab light chain of enhancing antibody | protein | 213 | 6% helix, 51% strand | — |
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 | 1042 | 0.73 | 0.77 | 96 | empty |
| 2 | 944 | 0.72 | 0.77 | 94 | empty |
| 3 | 836 | 0.72 | 0.78 | 93 | empty |
| 4 | 836 | 0.70 | 0.77 | 109 | empty |
| 5 | 803 | 0.70 | 0.77 | 98 | empty |
Interfaces
6 interfaces between chains.
- B–C · 1149 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 953 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 910 Ų buried · 12 hydrogen bonds · protein-protein
- H–L · 187 Ų buried · 0 hydrogen bonds · protein-protein
- C–H · 93 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 7DZX · Spike protein from SARS-CoV2 with Fab fragment of enhancing antibody 8D2 · 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 7DZX · PDBe 7DZX · UniProt P0DTC2
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