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Crystal structure of the human coronavirus 229E spike protein receptor binding domain in complex with human aminopeptidase N
Analyse Crystal structure of the human coronavirus 229E spike protein receptor binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ATK
- Type
- protein
- Length
- 2,898 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aminopeptidase N; Spike glycoprotein
- EC
- 3.4.11.2
- UniProt
- P15144, P15423
- Ligands
- NAG, ZN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 41% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Aminopeptidase N (EC 3.4.11.2) | protein | 892 | 47% helix, 20% strand | P15144 |
| C | Aminopeptidase N (EC 3.4.11.2) | protein | 891 | 46% helix, 20% strand | P15144 |
| E | Spike glycoprotein | protein | 134 | 0% helix, 44% strand | P15423 |
| D | Spike glycoprotein | protein | 78 | 0% helix, 29% strand | P15423 |
| F | Spike glycoprotein | protein | 11 | 0% helix, 9% strand | P15423 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 25 copies · chains A, B, C, E, D
- ZN · Zinc ion · metal · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1097 | 0.80 | 0.82 | 115 | ZN |
| 2 | 1171 | 0.80 | 0.82 | 108 | empty |
| 3 | 1007 | 0.78 | 0.80 | 74 | empty |
| 4 | 485 | 0.76 | 0.84 | 63 | empty |
| 5 | 501 | 0.76 | 0.84 | 53 | empty |
Interfaces
5 interfaces between chains.
- A–B · 911 Ų buried · 4 hydrogen bonds · protein-protein
- B–E · 522 Ų buried · 11 hydrogen bonds · protein-protein
- A–D · 517 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 474 Ų buried · 8 hydrogen bonds · protein-protein
- C–F · 374 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 glycan, 12 disulfide (N-glycosylation, disulfide).
Compared structures
- 6ATK · Crystal structure of the human coronavirus 229E spike protein receptor binding domain in… · 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 B 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 P15144
- Every structure of UniProt P15423
- Elsewhere: RCSB PDB 6ATK · PDBe 6ATK · UniProt P15144 · UniProt P15423
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