Research workbench
S-2H2-F1 structure, one rbd is up and two rbds are down, only up rbd binds with a 2H2 Fab
Analyse S-2H2-F1 structure, one rbd is up and two rbds are down, only up rbd binds with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7DK5
- Type
- protein
- Length
- 3,608 residues
- Chains
- 5
- 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 0.82
Structure
electron microscopy · 4 distinct chains · 18% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 1060 | 21% helix, 31% strand | P0DTC2 |
| C, B | Spike glycoprotein | protein | 1058 | 21% helix, 31% strand | P0DTC2 |
| a | The heavy chain of 2H2 Fab | protein | 214 | 4% helix, 43% strand | — |
| b | The light chain of 2H2 Fab | protein | 218 | 5% helix, 39% 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 | 579 | 0.82 | 0.88 | 79 | empty |
| 2 | 713 | 0.78 | 0.82 | 89 | empty |
| 3 | 800 | 0.78 | 0.81 | 73 | empty |
| 4 | 515 | 0.76 | 0.84 | 49 | empty |
| 5 | 728 | 0.76 | 0.81 | 97 | empty |
Interfaces
6 interfaces between chains.
- C–B · 5174 Ų buried · 55 hydrogen bonds · protein-protein
- A–B · 4434 Ų buried · 37 hydrogen bonds · protein-protein
- A–C · 3998 Ų buried · 44 hydrogen bonds · protein-protein
- a–b · 1884 Ų buried · 15 hydrogen bonds · protein-protein
- A–b · 880 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 7DK5 · S-2H2-F1 structure, one RBD is up and two RBDs are down, only up RBD binds with a 2H2 Fab · the same entry in another collection · chain b against b, 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 7DK5 · PDBe 7DK5 · UniProt P0DTC2
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