MolNFT v1 · #191349 · protein

SARS-cov-2 receptor-binding domain speedesign immunogen 1 bound to C144 scfv

8DCE: “SARS-cov-2 receptor-binding domain speedesign immunogen 1 bound to C144 scfv”. X-ray diffraction, 2 pockets (best druggability 0.59). MolNFT v1 #191349 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 8DCE
Type: protein
Length: 436 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: C144 scfv; Spike protein S1
UniProt: P0DTC2
Pockets: 2 · best druggability 0.59

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 40% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	C144 scfv	protein	242	4% helix, 47% strand	—
A	Spike protein S1	protein	194	18% helix, 31% strand	P0DTC2

Pockets

2 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	376	0.59	0.76	44	empty
2	115	0.37	0.74	29	empty

Interfaces

1 interface between chains.

H–A · 844 Å² buried · 23 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

8DCE · SARS-CoV-2 Receptor-Binding Domain SPEEDesign Immunogen 1 Bound to C144 scFv · 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 8DCE · PDBe 8DCE · UniProt P0DTC2

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