Research workbench
Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with its human receptor
Analyse Crystal structure of NL63 respiratory coronavirus receptor-binding domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KBH
- Type
- protein
- Length
- 2,812 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Angiotensin-converting enzyme 2; Spike glycoprotein
- EC
- 3.4.17.-
- UniProt
- Q9BYF1, Q6Q1S2
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.71
Structure
x-ray diffraction · 2 distinct chains · 49% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, C, D | Angiotensin-converting enzyme 2 (EC 3.4.17.-) | protein | 593 | 58% helix, 4% strand | Q9BYF1 |
| E, F, G, H | Spike glycoprotein | protein | 110 | 0% helix, 48% strand | Q6Q1S2 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, E, B, F, C, G, D, H
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 | 482 | 0.71 | 0.81 | 65 | empty |
| 2 | 369 | 0.69 | 0.82 | 49 | empty |
| 3 | 340 | 0.68 | 0.82 | 46 | empty |
| 4 | 347 | 0.65 | 0.80 | 35 | empty |
| 5 | 353 | 0.65 | 0.80 | 36 | empty |
Interfaces
9 interfaces between chains.
- B–F · 716 Ų buried · 5 hydrogen bonds · protein-protein
- C–G · 712 Ų buried · 5 hydrogen bonds · protein-protein
- A–E · 684 Ų buried · 4 hydrogen bonds · protein-protein
- D–H · 680 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 481 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 16 glycan (disulfide, N-glycosylation).
Compared structures
- 3KBH · Crystal structure of NL63 respiratory coronavirus receptor-binding domain complexed with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BYF1 · AlphaFold monomer V2.0 prediction for angiotensin-converting enzyme 2 (Q9BYF1) · a predicted model of the same protein · chain C 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 Q9BYF1
- Every structure of UniProt Q6Q1S2
- Elsewhere: RCSB PDB 3KBH · PDBe 3KBH · UniProt Q9BYF1 · UniProt Q6Q1S2
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