MolNFT v2 · #198753 · protein
SARS-CoV-2 Delta S-RBD-8D3
7W9F · The heavy chain of 8D3: “SARS-CoV-2 Delta S-RBD-8D3”. Electron microscopy at 3.6, 3 pockets (best druggability 0.64). MolNFT v2 #198753 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7W9F
- Type
- protein
- Length
- 625 residues
- Chains
- 3
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.6
- Source
- Mus musculus; Severe acute respiratory syndrome coronavirus 2
- Molecule
- The heavy chain of 8D3; The light chain of 8D3; Spike protein S1
- UniProt
- P0DTC2
- Pockets
- 3 · best druggability 0.64
Structure
electron microscopy · resolution 3.6 · 3 distinct chains · 6% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | The heavy chain of 8D3 | protein | 220 | 5% helix, 44% strand | — |
| B | The light chain of 8D3 | protein | 211 | 5% helix, 44% strand | — |
| E | Spike protein S1 | protein | 194 | 6% helix, 25% strand | P0DTC2 |
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.64 | 0.75 | 62 | empty |
| 2 | 160 | 0.46 | 0.76 | 31 | empty |
| 3 | 85 | 0.33 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1909 Ų buried · 16 hydrogen bonds · protein-protein
- A–E · 506 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 227 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 7W9F · SARS-cov-2 delta S-rbd-8D3 · 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 7W9F · PDBe 7W9F · UniProt P0DTC2
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