MolNFT v1 · #171271 · protein

H11-D4 complex with SARS-cov-2 rbd

6YZ5 · Spike glycoprotein: “H11-D4 complex with SARS-cov-2 rbd”. X-ray diffraction, 1 ligand (NAG), 1 pocket (best druggability 0.46). MolNFT v1 #171271 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6YZ5
Type: protein
Length: 322 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Spike glycoprotein; Nanobody H11-D4
UniProt: P0DTC2
Ligands: NAG
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 2 distinct chains · 14% helix, 37% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Spike glycoprotein	protein	195	17% helix, 30% strand	P0DTC2
F	Nanobody H11-D4	protein	127	9% helix, 47% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
EDO · 1,2-ethanediol · additive · 12 copies · chains E, F
ACT · Acetate ion · additive · 4 copies · chains E, F

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	166	0.46	0.76	32	EDO

Interfaces

1 interface between chains.

E–F · 690 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

6YZ5 · H11-D4 complex with SARS-CoV-2 RBD · the same entry in another collection · chain E against E, 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 6YZ5 · PDBe 6YZ5 · UniProt P0DTC2

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.