MolNFT v1 · #189815 · protein
SARS-cov-2 kappa variant spike protein in C3 state
7VXC · Spike glycoprotein: “SARS-cov-2 kappa variant spike protein in C3 state”. Electron microscopy, 20 pockets (best druggability 0.84). MolNFT v1 #189815 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VXC
- Type
- protein
- Length
- 3,801 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Spike glycoprotein; Angiotensin-converting enzyme 2
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- P0DTC2, Q9BYF1
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, A, B | Spike glycoprotein | protein | 1068 | 20% helix, 30% strand | P0DTC2 |
| C | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 597 | 59% helix, 4% strand | Q9BYF1 |
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 | 774 | 0.84 | 0.87 | 89 | empty |
| 2 | 1091 | 0.83 | 0.84 | 120 | empty |
| 3 | 352 | 0.82 | 0.92 | 50 | empty |
| 4 | 993 | 0.81 | 0.82 | 122 | empty |
| 5 | 618 | 0.78 | 0.84 | 56 | empty |
Interfaces
4 interfaces between chains.
- A–B · 4194 Ų buried · 32 hydrogen bonds · protein-protein
- D–B · 4131 Ų buried · 31 hydrogen bonds · protein-protein
- D–A · 4023 Ų buried · 40 hydrogen bonds · protein-protein
- D–C · 1002 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 7VXC · SARS-CoV-2 Kappa variant spike protein in C3 state · the same entry in another collection · chain D against D, TM-score 1.00
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain C against A, TM-score 0.98
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against A, TM-score 0.98
- 3SCI · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against A, TM-score 0.98
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C against A, TM-score 0.98
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain C 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 C 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 C 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 7VXC · PDBe 7VXC · UniProt P0DTC2 · UniProt Q9BYF1
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