Research workbench
Cryo-EM structure of omicron rbd complexed with ACE2 and 304 Fab
Analyse Cryo-EM structure of omicron rbd complexed with ACE2 and 304 Fab in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XCP
- Type
- protein
- Length
- 1,017 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Processed angiotensin-converting enzyme 2; Spike protein S1; Heavy chain of 304 Fab…
- UniProt
- Q9BYF1, P0DTC2
- Ligands
- NAG, ZN
- Pockets
- 11 · best druggability 0.77
Structure
electron microscopy · 4 distinct chains · 38% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Processed angiotensin-converting enzyme 2 | protein | 596 | 60% helix, 4% strand | Q9BYF1 |
| B | Spike protein S1 | protein | 195 | 12% helix, 28% strand | P0DTC2 |
| H | Heavy chain of 304 Fab | protein | 118 | 5% helix, 56% strand | — |
| L | Lignt chain of 304 Fab | protein | 108 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, H, B
- ZN · Zinc ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 931 | 0.77 | 0.80 | 96 | ZN |
| 2 | 400 | 0.63 | 0.78 | 42 | empty |
| 3 | 211 | 0.62 | 0.82 | 32 | empty |
| 4 | 89 | 0.41 | 0.78 | 22 | empty |
| 5 | 91 | 0.40 | 0.77 | 16 | empty |
Interfaces
5 interfaces between chains.
- A–B · 989 Ų buried · 23 hydrogen bonds · protein-protein
- H–L · 907 Ų buried · 7 hydrogen bonds · protein-protein
- B–H · 583 Ų buried · 4 hydrogen bonds · protein-protein
- B–L · 439 Ų buried · 10 hydrogen bonds · protein-protein
- A–H · 19 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 7XCP · Cryo-EM structure of Omicron RBD complexed with ACE2 and 304 Fab · the same entry in another collection · chain B against B, TM-score 1.00
- 3SCJ · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A 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 A against A, TM-score 0.99
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A against A, TM-score 0.99
- 3SCK · Crystal structure of spike protein receptor-binding domain from a predicted SARS… · a predicted model of the same protein · chain A 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 A 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 A against A, TM-score 0.99
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain A 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 7XCP · PDBe 7XCP · UniProt Q9BYF1 · UniProt P0DTC2
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