Research workbench

SARS-cov-2 delta S-rbd-8D3

Analyse SARS-cov-2 delta S-rbd-8D3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7W9F
Type: protein
Length: 625 residues
Chains: 3
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: The heavy chain of 8D3; The light chain of 8D3; Spike protein S1
UniProt: P0DTC2
Pockets: 3 · best druggability 0.64

Structure

electron microscopy · 3 distinct chains · 6% helix, 38% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	The heavy chain of 8D3	protein	220	5% helix, 44% strand	—
B	The light chain of 8D3	protein	211	5% helix, 44% strand	—
E	Spike protein S1	protein	194	6% helix, 25% strand	P0DTC2

Pockets

3 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	619	0.64	0.75	62	empty
2	160	0.46	0.76	31	empty
3	85	0.33	0.74	14	empty

Interfaces

3 interfaces between chains.

A–B · 1909 Å² buried · 16 hydrogen bonds · protein-protein
A–E · 506 Å² buried · 7 hydrogen bonds · protein-protein
B–E · 227 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide (disulfide).

Compared structures

7W9F · SARS-CoV-2 Delta S-RBD-8D3 · 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 P0DTC2
Elsewhere: RCSB PDB 7W9F · PDBe 7W9F · UniProt P0DTC2

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