MolNFT v1 · #179892 · protein
SARS-cov-2 spike glycoprotein with three ACE2 bound
7KJ4: “SARS-cov-2 spike glycoprotein with three ACE2 bound”. Electron microscopy, 1 ligand (NAG), 20 pockets (best druggability 0.85). MolNFT v1 #179892 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 7KJ4
- Type
- protein
- Length
- 4,722 residues
- Chains
- 6
- 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
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · 2 distinct chains · 37% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C | Spike glycoprotein | protein | 981 | 22% helix, 32% strand | P0DTC2 |
| D, E, F | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 593 | 61% helix, 4% strand | Q9BYF1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 90 copies · chains A, B, C, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
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 | 670 | 0.85 | 0.89 | 85 | empty |
| 2 | 781 | 0.85 | 0.88 | 75 | empty |
| 3 | 826 | 0.85 | 0.87 | 94 | empty |
| 4 | 472 | 0.75 | 0.84 | 41 | empty |
| 5 | 795 | 0.73 | 0.78 | 58 | empty |
Interfaces
6 interfaces between chains.
- A–B · 4497 Ų buried · 38 hydrogen bonds · protein-protein
- B–C · 4466 Ų buried · 39 hydrogen bonds · protein-protein
- A–C · 4455 Ų buried · 39 hydrogen bonds · protein-protein
- C–E · 1054 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 972 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 52 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KJ4 · SARS-CoV-2 Spike Glycoprotein with three ACE2 Bound · 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 E 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 E 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 E 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 E against A, TM-score 0.99
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 7KJ4 · PDBe 7KJ4 · UniProt P0DTC2 · UniProt Q9BYF1
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