MolNFT v1 · #176361 · protein
S-2H2-F3B structure, three rbds are up and each rbd binds with a 2H2 Fab.
7DK7 · The heavy chain fragment of 2H2 Fab: “S-2H2-F3B structure, three rbds are up and each rbd binds with a 2H2 Fab.”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #176361 on GenesisL1: 3D structure, binding sites…
- PDB
- 7DK7
- Type
- protein
- Length
- 4,181 residues
- Chains
- 9
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- The heavy chain fragment of 2H2 Fab; The light chain fragment of 2H2 Fab; Spike…
- UniProt
- P0DTC2
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 5 distinct chains · 14% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| e | The heavy chain fragment of 2H2 Fab | protein | 18 | 0% helix, 39% strand | — |
| f | The light chain fragment of 2H2 Fab | protein | 119 | 0% helix, 41% strand | — |
| A, B, C | Spike glycoprotein | protein | 1060 | 20% helix, 31% strand | P0DTC2 |
| a, c | The heavy chain fragment of 2H2 Fab | protein | 214 | 4% helix, 46% strand | — |
| b, d | The light chain fragment of 2H2 Fab | protein | 218 | 3% helix, 45% 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 | 674 | 0.84 | 0.88 | 72 | empty |
| 2 | 436 | 0.79 | 0.87 | 37 | empty |
| 3 | 1040 | 0.78 | 0.80 | 84 | empty |
| 4 | 865 | 0.76 | 0.79 | 77 | empty |
| 5 | 199 | 0.74 | 0.90 | 33 | empty |
Interfaces
12 interfaces between chains.
- B–C · 4960 Ų buried · 48 hydrogen bonds · protein-protein
- A–C · 4729 Ų buried · 45 hydrogen bonds · protein-protein
- A–B · 4380 Ų buried · 41 hydrogen bonds · protein-protein
- a–b · 2138 Ų buried · 13 hydrogen bonds · protein-protein
- c–d · 2039 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 45 disulfide (disulfide).
Compared structures
- 7DK7 · S-2H2-F3b structure, three RBDs are up and each RBD binds with a 2H2 Fab. · the same entry in another collection · chain e against e, 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 7DK7 · PDBe 7DK7 · UniProt P0DTC2
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