MolNFT v2 · #198838 · protein
Crystal structure of the SARS-Cov-2 RBD in complex with Fab 2303
7WBZ · Spike protein S1: “Crystal structure of the SARS-Cov-2 RBD in complex with Fab 2303”. X-ray diffraction at 2.42, 1 ligand (NAG), 6 pockets (best druggability 0.61). MolNFT v2 #198838 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7WBZ
- Type
- protein
- Length
- 625 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.42
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike protein S1; 2303 heavy chain; 2303 light chain
- UniProt
- P0DTC2
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.61
Structure
x-ray diffraction · resolution 2.42 · 3 distinct chains · 11% helix, 44% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike protein S1 | protein | 194 | 17% helix, 30% strand | P0DTC2 |
| H | 2303 heavy chain | protein | 216 | 10% helix, 51% strand | — |
| L | 2303 light chain | protein | 215 | 6% helix, 49% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 275 | 0.61 | 0.79 | 28 | empty |
| 2 | 253 | 0.59 | 0.79 | 36 | empty |
| 3 | 332 | 0.54 | 0.75 | 38 | empty |
| 4 | 106 | 0.41 | 0.76 | 19 | empty |
| 5 | 62 | 0.30 | 0.74 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1801 Ų buried · 15 hydrogen bonds · protein-protein
- A–H · 813 Ų buried · 17 hydrogen bonds · protein-protein
- A–L · 488 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7WBZ · Crystal structure of the SARS-cov-2 rbd in complex with Fab 2303 · 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 7WBZ · PDBe 7WBZ · UniProt P0DTC2
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