Research workbench

Ccov-hupn-2018 S in the proximal conformation (local refinement of domain 0)

Analyse Ccov-hupn-2018 S in the proximal conformation (local refinement of domain 0) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7US9
Type: protein
Length: 145 residues
Chains: 1
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein
UniProt: A0A8E6CMP0
Ligands: NAG
Pockets: 4 · best druggability 0.53

Structure

electron microscopy · 1 distinct chain · 8% helix, 54% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	145	8% helix, 54% strand	A0A8E6CMP0

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	63	0.53	0.86	17	empty
2	78	0.49	0.83	17	empty
3	66	0.43	0.81	15	empty
4	54	0.36	0.78	13	empty

Modifications

Observed in the structure: 3 glycan, 1 disulfide (N-glycosylation, disulfide).

Compared structures

7US9 · CCoV-HuPn-2018 S in the proximal conformation (local refinement of domain 0) · the same entry in another collection · chain A 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 A0A8E6CMP0
Elsewhere: RCSB PDB 7US9 · PDBe 7US9 · UniProt A0A8E6CMP0

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