Research workbench
SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured ACE2 mimetic CVD432
Analyse SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to linker variant of affinity matured… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DV1
- Type
- protein
- Length
- 796 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.4
- Source
- Homo sapiens; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chain…
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- P0DTC2, Q9BYF1, P0DOX5
- Ligands
- NAG
- Pockets
- 6 · best druggability 0.69
Structure
electron microscopy · resolution 3.4 · 2 distinct chains · 50% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 201 | 16% helix, 28% strand | P0DTC2 |
| D | Angiotensin-converting enzyme 2,Immunoglobulin gamma-1 heavy chain fusion,Immunoglobulin gamma-1 heavy chain (EC 3.4.17.23, 3.4.17.-) | protein | 595 | 62% helix, 3% strand | Q9BYF1, P0DOX5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, D
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 | 440 | 0.69 | 0.81 | 42 | empty |
| 2 | 513 | 0.67 | 0.78 | 53 | empty |
| 3 | 293 | 0.64 | 0.81 | 37 | empty |
| 4 | 70 | 0.36 | 0.77 | 15 | empty |
| 5 | 58 | 0.32 | 0.76 | 15 | empty |
Interfaces
1 interface between chains.
- A–D · 846 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 8DV1 · SARS-cov-2 wuhan-hu-1-spike-rbd bound to linker variant of affinity matured ACE2 mimetic… · the same entry in another collection · chain D against D, TM-score 1.00
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.99
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.98
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain D against A, TM-score 0.98
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain D against A, TM-score 0.98
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
- Every structure of UniProt Q9BYF1
- Every structure of UniProt P0DOX5
- Elsewhere: RCSB PDB 8DV1 · PDBe 8DV1 · UniProt P0DTC2 · UniProt Q9BYF1 · UniProt P0DOX5
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