Research workbench
SARS-cov-2 wuhan-hu-1-spike-rbd bound to computationally engineered ACE2 mimetic CVD293
Analyse SARS-cov-2 wuhan-hu-1-spike-rbd bound to computationally engineered ACE2… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8DV2
- Type
- protein
- Length
- 796 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2,IMMUNOGLOBULIN gamma-1 heavy chain…
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- P0DTC2, Q9BYF1
- Pockets
- 5 · best druggability 0.69
Structure
electron microscopy · 2 distinct chains · 47% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Spike glycoprotein | protein | 201 | 13% helix, 26% strand | P0DTC2 |
| D | Angiotensin-converting enzyme 2,IMMUNOGLOBULIN gamma-1 heavy chain fusion (EC 3.4.17.23, 3.4.17.-) | protein | 595 | 59% helix, 5% strand | Q9BYF1 |
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 834 | 0.69 | 0.75 | 65 | empty |
| 2 | 555 | 0.67 | 0.77 | 54 | empty |
| 3 | 324 | 0.65 | 0.80 | 37 | empty |
| 4 | 93 | 0.36 | 0.75 | 32 | empty |
| 5 | 52 | 0.25 | 0.73 | 12 | empty |
Interfaces
1 interface between chains.
- A–D · 853 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 8DV2 · SARS-CoV-2 Wuhan-hu-1-Spike-RBD bound to computationally engineered ACE2 mimetic CVD293 · 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 0.99
- 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 0.99
- 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
- Elsewhere: RCSB PDB 8DV2 · PDBe 8DV2 · UniProt P0DTC2 · UniProt Q9BYF1
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