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Local structure of BD55-3372 and delta spike

Analyse Local structure of BD55-3372 and delta spike in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7WRO
Type: protein
Length: 412 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: 3372H; 3372L; Spike protein S1
UniProt: P0DTC2
Pockets: 5 · best druggability 0.44

Structure

electron microscopy · 3 distinct chains · 7% helix, 30% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	3372H	protein	118	5% helix, 47% strand	—
L	3372L	protein	111	0% helix, 30% strand	—
R	Spike protein S1	protein	183	11% helix, 19% strand	P0DTC2

Pockets

5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	164	0.44	0.75	35	empty
2	62	0.42	0.81	14	empty
3	67	0.30	0.74	14	empty
4	62	0.28	0.73	17	empty
5	63	0.27	0.73	14	empty

Interfaces

3 interfaces between chains.

H–L · 858 Å² buried · 16 hydrogen bonds · protein-protein
H–R · 503 Å² buried · 11 hydrogen bonds · protein-protein
L–R · 235 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

7WRO · Local structure of BD55-3372 and delta spike · the same entry in another collection · chain H against H, 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 P0DTC2
Elsewhere: RCSB PDB 7WRO · PDBe 7WRO · UniProt P0DTC2

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