MolNFT v1 · #176360 · protein
S-2H2-F2 structure, two rbds are up and one rbd is down, each up rbd binds with a 2H2 Fab.
7DK6 · Spike glycoprotein: “S-2H2-F2 structure, two rbds are up and one rbd is down, each up rbd binds with a 2H2 Fab.”. Electron microscopy, 20 pockets (best druggability 0.83). MolNFT v1 #176360 on GenesisL1: 3D structure, binding sites…
- PDB
- 7DK6
- Type
- protein
- Length
- 4,042 residues
- Chains
- 7
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; The heavy chain of 2H2 Fab; The light chain of 2H2 Fab
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 18% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 1060 | 21% helix, 32% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1058 | 21% helix, 32% strand | P0DTC2 |
| a, c | The heavy chain of 2H2 Fab | protein | 214 | 6% helix, 46% strand | — |
| b, d | The light chain of 2H2 Fab | protein | 218 | 5% helix, 42% 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 | 621 | 0.83 | 0.88 | 79 | empty |
| 2 | 692 | 0.83 | 0.87 | 92 | empty |
| 3 | 624 | 0.80 | 0.85 | 81 | empty |
| 4 | 419 | 0.77 | 0.86 | 40 | empty |
| 5 | 323 | 0.76 | 0.87 | 33 | empty |
Interfaces
9 interfaces between chains.
- B–C · 5454 Ų buried · 64 hydrogen bonds · protein-protein
- A–C · 5002 Ų buried · 53 hydrogen bonds · protein-protein
- A–B · 4960 Ų buried · 55 hydrogen bonds · protein-protein
- c–d · 1858 Ų buried · 15 hydrogen bonds · protein-protein
- a–b · 1762 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 46 disulfide (disulfide).
Compared structures
- 7DK6 · S-2H2-F2 structure, two RBDs are up and one RBD is down, each up RBD binds with a 2H2 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 7DK6 · PDBe 7DK6 · UniProt P0DTC2
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