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Crystal structure of SARS-cov spike receptor-binding domain complexed with neutralizing antibody

Analyse Crystal structure of SARS-cov spike receptor-binding domain complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VMU
Type: protein
Length: 396 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Scfv E4; Spike protein S1
UniProt: P0DTC2
Pockets: 3 · best druggability 0.52

Structure

x-ray diffraction · 2 distinct chains · 10% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Scfv E4	protein	220	7% helix, 49% strand	—
B	Spike protein S1	protein	176	14% helix, 27% 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	112	0.52	0.82	20	empty
2	72	0.29	0.72	20	empty
3	57	0.27	0.73	12	empty

Interfaces

1 interface between chains.

A–B · 1263 Å² buried · 30 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

7VMU · Crystal Structure of SARS-CoV Spike Receptor-Binding Domain Complexed with Neutralizing… · 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 7VMU · PDBe 7VMU · UniProt P0DTC2

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