MolNFT v1 · #179803 · protein

Crystal structure of synthetic nanobody (SB45) complexes with SARS- cov-2 receptor binding domain

7KGJ · Spike glycoprotein: “Crystal structure of synthetic nanobody (SB45) complexes with SARS- cov-2 receptor binding domain”. X-ray diffraction, 2 pockets (best druggability 0.44). MolNFT v1 #179803 on GenesisL1: 3D structure, binding…

PDB: 7KGJ
Type: protein
Length: 317 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; SB45, sybody-45, synthetic nanobody
UniProt: P0DTC2
Pockets: 2 · best druggability 0.44

Structure

x-ray diffraction · 2 distinct chains · 13% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Spike glycoprotein	protein	196	18% helix, 30% strand	P0DTC2
B	SB45, sybody-45, synthetic nanobody	protein	121	5% helix, 55% strand	—

Pockets

2 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	111	0.44	0.78	25	empty
2	72	0.34	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 1044 Å² buried · 17 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide (disulfide).

Compared structures

7KGJ · Crystal structure of synthetic nanobody (Sb45) complexes with SARS-CoV-2 receptor binding… · 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 7KGJ · PDBe 7KGJ · UniProt P0DTC2

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