MolNFT v1 · #189661 · protein
Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of virus adaptation to humans
7VPQ · Aminopeptidase N: “Structures of a deltacoronavirus spike protein bound to porcine and human receptors indicate the risk of…”. X-ray diffraction, 2 ligands (NAG, ZN), 20 pockets (best druggability 0.81). MolNFT v1 #189661 on…
- PDB
- 7VPQ
- Type
- protein
- Length
- 2,991 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N; Spike protein
- EC
- 3.4.11.2
- UniProt
- P15144, A0A4P8D758
- Ligands
- NAG, ZN
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 42% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Aminopeptidase N (EC 3.4.11.2) | protein | 895 | 45% helix, 20% strand | P15144 |
| B, D, F | Spike protein | protein | 103 | 0% helix, 51% strand | A0A4P8D758 |
| E | Aminopeptidase N (EC 3.4.11.2) | protein | 892 | 45% helix, 20% strand | P15144 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 30 copies · chains A, C, E, B, D, F
- ZN · Zinc ion · metal · 3 copies · chains A, C, E
- GOL · Glycerol · additive · 3 copies · chains A, C, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 701 | 0.81 | 0.85 | 93 | empty |
| 2 | 845 | 0.79 | 0.82 | 98 | empty |
| 3 | 957 | 0.79 | 0.81 | 69 | empty |
| 4 | 664 | 0.76 | 0.82 | 65 | ZN |
| 5 | 418 | 0.74 | 0.84 | 51 | empty |
Interfaces
6 interfaces between chains.
- A–C · 1079 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 997 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 988 Ų buried · 18 hydrogen bonds · protein-protein
- E–F · 974 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 479 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 glycan, 9 disulfide (N-glycosylation, disulfide).
Compared structures
- 7VPQ · Structures of a deltacoronavirus spike protein bound to porcine and human receptors… · the same entry in another collection · chain F against F, TM-score 1.00
- P15144 · AlphaFold monomer V2.0 prediction for aminopeptidase N (P15144) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 P15144
- Every structure of UniProt A0A4P8D758
- Elsewhere: RCSB PDB 7VPQ · PDBe 7VPQ · UniProt P15144 · UniProt A0A4P8D758
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