Research workbench
ACE2-rbd focused refinement using symmetry expansion of applied C3 for triple ACE2-bound SARS-cov-2 trimer spike at pH 7.4
Analyse ACE2-rbd focused refinement using symmetry expansion of applied C3 for triple… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KMB
- Type
- protein
- Length
- 788 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme 2; Spike glycoprotein
- EC
- 3.4.17.23, 3.4.17.-
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG
- Pockets
- 8 · best druggability 0.71
Structure
electron microscopy · 2 distinct chains · 45% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 596 | 55% helix, 3% strand | Q9BYF1 |
| G | Spike glycoprotein | protein | 192 | 13% helix, 18% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains F, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 424 | 0.71 | 0.82 | 47 | empty |
| 2 | 56 | 0.66 | 0.94 | 19 | empty |
| 3 | 307 | 0.64 | 0.80 | 36 | empty |
| 4 | 246 | 0.50 | 0.75 | 30 | empty |
| 5 | 112 | 0.48 | 0.80 | 24 | empty |
Interfaces
1 interface between chains.
- F–G · 1010 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 7 glycan (disulfide, N-glycosylation).
Compared structures
- 7KMB · ACE2-RBD Focused Refinement Using Symmetry Expansion of Applied C3 for Triple ACE2-bound… · the same entry in another collection · chain F against F, TM-score 1.00
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain F 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 F 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 F against A, TM-score 0.97
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against A, TM-score 0.97
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against A, TM-score 0.97
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against A, TM-score 0.97
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain F against A, TM-score 0.97
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 Q9BYF1
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7KMB · PDBe 7KMB · UniProt Q9BYF1 · UniProt P0DTC2
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