MolNFT v2 · #225465 · protein
BA.2.86 Spike in complex with bovine ACE2 (bound 1 ACE2)
8XZ8 · Angiotensin-converting enzyme: “BA.2.86 Spike in complex with bovine ACE2 (bound 1 ACE2)”. Electron microscopy at 3.65, 4 ligands (NAG, BMA, ZN), 20 pockets (best druggability 0.85). MolNFT v2 #225465 on GenesisL1: 3D structure…
- PDB
- 8XZ8
- Type
- protein
- Length
- 3,785 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.65
- Source
- Bos taurus; Severe acute respiratory syndrome coronavirus 2
- Molecule
- Angiotensin-converting enzyme; Spike glycoprotein
- EC
- 3.4.-.-
- UniProt
- Q2HJI5, P0DTC2
- Ligands
- NAG, BMA, ZN, CL
- Pockets
- 20 · best druggability 0.85
Structure
electron microscopy · resolution 3.65 · 2 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Angiotensin-converting enzyme (EC 3.4.-.-) | protein | 596 | 61% helix, 3% strand | Q2HJI5 |
| B, C, D | Spike glycoprotein | protein | 1063 | 22% helix, 25% strand | P0DTC2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 53 copies · chains B, C, D, A
- BMA · beta-D-mannopyranose · sugar · 17 copies · chains D
- ZN · Zinc ion · metal · chains A
- CL · Chloride ion · ion · chains A
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 | 993 | 0.85 | 0.86 | 117 | empty |
| 2 | 811 | 0.84 | 0.87 | 89 | empty |
| 3 | 969 | 0.84 | 0.85 | 108 | empty |
| 4 | 571 | 0.81 | 0.87 | 79 | empty |
| 5 | 321 | 0.79 | 0.89 | 34 | empty |
Interfaces
4 interfaces between chains.
- B–D · 6615 Ų buried · 68 hydrogen bonds · protein-protein
- C–D · 6263 Ų buried · 52 hydrogen bonds · protein-protein
- B–C · 5493 Ų buried · 62 hydrogen bonds · protein-protein
- A–B · 1007 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 53 glycan, 38 disulfide (N-glycosylation, disulfide, glycosylation).
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 Q2HJI5
- Every structure of UniProt P0DTC2
- Elsewhere: RCSB PDB 8XZ8 · PDBe 8XZ8 · UniProt Q2HJI5 · UniProt P0DTC2
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