MolNFT v1 · #189814 · protein
SARS-cov-2 kappa variant spike protein in C2B state
7VXB · Spike glycoprotein: “SARS-cov-2 kappa variant spike protein in C2B state”. Electron microscopy, 20 pockets (best druggability 0.88). MolNFT v1 #189814 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7VXB
- Type
- protein
- Length
- 3,795 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 0.88
Structure
electron microscopy · 3 distinct chains · 29% helix, 25% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| D, B | Spike glycoprotein | protein | 1068 | 21% helix, 30% strand | P0DTC2 |
| C | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 597 | 59% helix, 4% strand | Q9BYF1 |
| A | Spike glycoprotein | protein | 1062 | 20% helix, 31% strand | P0DTC2 |
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 | 841 | 0.88 | 0.90 | 107 | empty |
| 2 | 939 | 0.84 | 0.85 | 105 | empty |
| 3 | 735 | 0.82 | 0.86 | 81 | empty |
| 4 | 959 | 0.81 | 0.83 | 98 | empty |
| 5 | 525 | 0.78 | 0.85 | 65 | empty |
Interfaces
4 interfaces between chains.
- A–B · 4337 Ų buried · 42 hydrogen bonds · protein-protein
- D–A · 4265 Ų buried · 37 hydrogen bonds · protein-protein
- D–B · 4182 Ų buried · 33 hydrogen bonds · protein-protein
- D–C · 1001 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 42 disulfide (disulfide).
Compared structures
- 7VXB · SARS-CoV-2 Kappa variant spike protein in C2b state · the same entry in another collection · chain C against C, 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 7VXB · PDBe 7VXB · UniProt P0DTC2 · UniProt Q9BYF1
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