Research workbench
The structure of PDCoV RBD and dog APN complex
Analyse The structure of PDCoV RBD and dog APN complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8YZI
- Type
- protein
- Length
- 2,030 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.05
- Source
- Canis lupus familiaris; Porcine deltacoronavirus
- Molecule
- Spike protein; Aminopeptidase N
- EC
- 3.4.11.2
- UniProt
- A0A0E3N634, P79143
- Ligands
- NAG, BMA, ZN
- Pockets
- 20 · best druggability 0.81
Structure
electron microscopy · resolution 3.05 · 2 distinct chains · 39% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A | Spike protein | protein | 115 | 5% helix, 62% strand | A0A0E3N634 |
| B, D | Aminopeptidase N (EC 3.4.11.2) | protein | 900 | 44% helix, 19% strand | P79143 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 26 copies · chains B, D, C, A
- BMA · beta-D-mannopyranose · sugar
- ZN · Zinc ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1055 | 0.81 | 0.82 | 84 | empty |
| 2 | 608 | 0.80 | 0.85 | 64 | empty |
| 3 | 507 | 0.77 | 0.85 | 51 | empty |
| 4 | 107 | 0.75 | 0.94 | 29 | empty |
| 5 | 446 | 0.74 | 0.84 | 63 | empty |
Interfaces
3 interfaces between chains.
- B–D · 960 Ų buried · 0 hydrogen bonds · protein-protein
- C–B · 943 Ų buried · 13 hydrogen bonds · protein-protein
- A–D · 926 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan, 8 disulfide (N-glycosylation, disulfide).
Compared structures
- P79143 · AlphaFold monomer V2.0 prediction for aminopeptidase N (P79143) · a predicted model of the same protein · chain D against A, TM-score 0.98
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 A0A0E3N634
- Every structure of UniProt P79143
- Elsewhere: RCSB PDB 8YZI · PDBe 8YZI · UniProt A0A0E3N634 · UniProt P79143
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