MolNFT v1 · #176358 · protein
S-2H2-F3A structure, two rbds are up and one rbd is down, each rbd binds with a 2H2 Fab.
7DK4 · The heavy chain of 2H2 Fab: “S-2H2-F3A structure, two rbds are up and one rbd is down, each rbd binds with a 2H2 Fab.”. Electron microscopy, 20 pockets (best druggability 0.87). MolNFT v1 #176358 on GenesisL1: 3D structure, binding…
- PDB
- 7DK4
- Type
- protein
- Length
- 4,470 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- The heavy chain of 2H2 Fab; The light chain of 2H2 Fab; Spike glycoprotein
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 16% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| a, c, e | The heavy chain of 2H2 Fab | protein | 214 | 1% helix, 44% strand | — |
| b, d, f | The light chain of 2H2 Fab | protein | 218 | 4% helix, 44% strand | — |
| A, B, C | Spike glycoprotein | protein | 1058 | 21% helix, 33% strand | P0DTC2 |
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 | 1003 | 0.87 | 0.88 | 108 | empty |
| 2 | 1106 | 0.85 | 0.86 | 110 | empty |
| 3 | 1127 | 0.81 | 0.83 | 104 | empty |
| 4 | 479 | 0.80 | 0.88 | 51 | empty |
| 5 | 134 | 0.80 | 0.97 | 38 | empty |
Interfaces
16 interfaces between chains.
- B–C · 5266 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 5048 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 5025 Ų buried · 59 hydrogen bonds · protein-protein
- e–f · 1823 Ų buried · 15 hydrogen bonds · protein-protein
- a–b · 1779 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 51 disulfide (disulfide).
Compared structures
- 7DK4 · S-2H2-F3a structure, two RBDs are up and one RBD is down, each RBD binds with a 2H2 Fab. · the same entry in another collection · chain d against d, 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 7DK4 · PDBe 7DK4 · UniProt P0DTC2
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