Research workbench
Cryo-EM structure of double ACE2-bound SARS-cov-2 trimer spike at pH 7.4
Analyse Cryo-EM structure of double ACE2-bound SARS-cov-2 trimer spike at pH 7.4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KMZ
- Type
- protein
- Length
- 4,260 residues
- Chains
- 5
- 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 0.83
Structure
electron microscopy · 4 distinct chains · 27% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Spike glycoprotein | protein | 1007 | 21% helix, 26% strand | P0DTC2 |
| A | Spike glycoprotein | protein | 1030 | 21% helix, 25% strand | P0DTC2 |
| E, D | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 57% helix, 3% strand | Q9BYF1 |
| B | Spike glycoprotein | protein | 1031 | 20% helix, 28% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 61 copies · chains C, A, B, E, D
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 | 1177 | 0.83 | 0.84 | 119 | empty |
| 2 | 668 | 0.82 | 0.86 | 75 | empty |
| 3 | 672 | 0.82 | 0.86 | 82 | empty |
| 4 | 131 | 0.79 | 0.96 | 29 | empty |
| 5 | 256 | 0.79 | 0.91 | 42 | empty |
Interfaces
5 interfaces between chains.
- C–A · 4904 Ų buried · 47 hydrogen bonds · protein-protein
- C–B · 4525 Ų buried · 31 hydrogen bonds · protein-protein
- A–B · 4407 Ų buried · 34 hydrogen bonds · protein-protein
- A–E · 851 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 834 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 57 glycan, 45 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KMZ · Cryo-EM structure of double ACE2-bound SARS-CoV-2 trimer Spike at pH 7.4 · 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 D against A, TM-score 0.97
- 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 0.96
- 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 0.96
- 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 0.95
- 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 0.95
- 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 0.95
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 7KMZ · PDBe 7KMZ · UniProt P0DTC2 · UniProt Q9BYF1
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