MolNFT v1 · #190513 · protein
The crystal structure of SARS-cov-2 omicron BA.1 variant rbd in complex with equine ACE2
7XBY · Angiotensin-converting enzyme: “The crystal structure of SARS-cov-2 omicron BA.1 variant rbd in complex with equine ACE2”. X-ray diffraction, 3 ligands (NAG, ZN, BR), 5 pockets (best druggability 0.66). MolNFT v1 #190513 on…
- PDB
- 7XBY
- Type
- protein
- Length
- 791 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme; Spike protein S1
- EC
- 3.4.-.-
- UniProt
- F6V9L3, P0DTC2
- Ligands
- NAG, ZN, BR
- Pockets
- 5 · best druggability 0.66
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme (EC 3.4.-.-) | protein | 596 | 63% helix, 5% strand | F6V9L3 |
| B | Spike protein S1 | protein | 195 | 15% helix, 27% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B
- ZN · Zinc ion · metal · chains A
- BR · Bromide ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.66 | 0.78 | 37 | empty |
| 2 | 581 | 0.64 | 0.75 | 55 | empty |
| 3 | 480 | 0.62 | 0.76 | 69 | empty |
| 4 | 95 | 0.47 | 0.80 | 18 | NAG |
| 5 | 56 | 0.27 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 882 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 7XBY · The crystal structure of SARS-CoV-2 Omicron BA.1 variant RBD in complex with equine ACE2 · the same entry in another collection · chain A against A, TM-score 1.00
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 F6V9L3
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 7XBY · PDBe 7XBY · UniProt F6V9L3 · UniProt P0DTC2
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