Research workbench

Crystal structure of human coronavirus 229E spike protein receptor-binding domain in complex with C04 Fab

Analyse Crystal structure of 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: 7VN9
Type: protein
Length: 1,113 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 4.49
Source: Homo sapiens; Human coronavirus 229E
Molecule: C04 Fab heavy chain; C04 Fab light chain; Spike glycoprotein S1
UniProt: P15423
Ligands: NAG, BMA
Pockets: 14 · best druggability 0.76

Structure

x-ray diffraction · resolution 4.49 · 6 distinct chains · 4% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	C04 Fab heavy chain	protein	218	3% helix, 50% strand	—
L	C04 Fab light chain	protein	213	6% helix, 51% strand	—
E	Spike glycoprotein S1	protein	134	0% helix, 49% strand	P15423
A	C04 Fab heavy chain	protein	215	4% helix, 46% strand	—
B	C04 Fab light chain	protein	198	6% helix, 38% strand	—
C	Spike glycoprotein S1	protein	135	0% helix, 49% strand	P15423

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains E, H, C
BMA · beta-D-mannopyranose · sugar · 2 copies

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	73	0.76	0.98	22	empty
2	936	0.73	0.77	76	empty
3	579	0.61	0.74	57	empty
4	92	0.56	0.86	29	empty
5	167	0.56	0.81	35	empty

Interfaces

9 interfaces between chains.

H–L · 2004 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 1891 Å² buried · 10 hydrogen bonds · protein-protein
H–E · 513 Å² buried · 4 hydrogen bonds · protein-protein
L–E · 494 Å² buried · 5 hydrogen bonds · protein-protein
B–C · 483 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide, 4 glycan (disulfide, N-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 P15423
Elsewhere: RCSB PDB 7VN9 · PDBe 7VN9 · UniProt P15423

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.