Research workbench
SARS-cov-2 omicron BA.1 variant spike trimer with two mouse ACE2 bound
Analyse SARS-cov-2 omicron BA.1 variant spike trimer with two mouse ACE2 bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7XO4
- Type
- protein
- Length
- 4,252 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, Q8R0I0
- Ligands
- NAG, ZN
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Spike glycoprotein | protein | 1024 | 21% helix, 30% strand | P0DTC2 |
| C | Spike glycoprotein | protein | 1022 | 19% helix, 30% strand | P0DTC2 |
| D, E | Angiotensin-converting enzyme 2 (EC 3.4.17.23, 3.4.17.-) | protein | 591 | 52% helix, 4% strand | Q8R0I0 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, B, C, D, E
- ZN · Zinc ion · metal · 2 copies · chains D, E
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 | 1028 | 0.87 | 0.88 | 113 | empty |
| 2 | 696 | 0.83 | 0.87 | 88 | empty |
| 3 | 842 | 0.82 | 0.85 | 109 | empty |
| 4 | 542 | 0.81 | 0.87 | 70 | empty |
| 5 | 386 | 0.79 | 0.88 | 53 | empty |
Interfaces
5 interfaces between chains.
- A–C · 4748 Ų buried · 39 hydrogen bonds · protein-protein
- B–C · 4273 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 3892 Ų buried · 36 hydrogen bonds · protein-protein
- B–E · 1239 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 739 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 39 glycan, 37 disulfide (N-glycosylation, disulfide).
Compared structures
- 7XO4 · SARS-CoV-2 Omicron BA.1 Variant Spike Trimer with two mouse ACE2 Bound · the same entry in another collection · chain B against B, TM-score 1.00
- Q8R0I0 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q8R0I0) · a predicted model of the same protein · chain E against A, TM-score 0.93
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 Q8R0I0
- Elsewhere: RCSB PDB 7XO4 · PDBe 7XO4 · UniProt P0DTC2 · UniProt Q8R0I0
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