MolNFT v1 · #189633 · protein

Crystal structure of SARS-cov-2 rbd in complex with ARBD5

7VOA · Alpaca nanobody: “Crystal structure of SARS-cov-2 rbd in complex with ARBD5”. X-ray diffraction, 1 ligand (NAG), 1 pocket (best druggability 0.39). MolNFT v1 #189633 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 7VOA
Type: protein
Length: 324 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Alpaca nanobody; Spike glycoprotein
UniProt: P0DTC2
Ligands: NAG
Pockets: 1 · best druggability 0.39

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Alpaca nanobody	protein	128	5% helix, 51% strand	—
B	Spike glycoprotein	protein	196	19% helix, 29% strand	P0DTC2

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	105	0.39	0.76	22	empty

Interfaces

1 interface between chains.

A–B · 735 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

7VOA · Crystal structure of SARS-CoV-2 RBD in complex with aRBD5 · 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 7VOA · PDBe 7VOA · UniProt P0DTC2

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