MolNFT v1 · #168684 · protein

Structure of hepatitis C virus envelope glycoprotein E2 core from genotype 6A bound to broadly neutralizing antibody U1

6WO3: “Structure of hepatitis C virus envelope glycoprotein E2 core from genotype 6A bound to broadly neutralizing…”. X-ray diffraction, 1 ligand (NAG), 6 pockets (best druggability 0.65). MolNFT v1 #168684 on GenesisL1: 3D structure…

PDB: 6WO3
Type: protein
Length: 582 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein E2; Fab U1 heavy chain; Fab U1 light chain
Ligands: NAG
Pockets: 6 · best druggability 0.65

Structure

x-ray diffraction · 3 distinct chains · 8% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Envelope glycoprotein E2	protein	148	11% helix, 36% strand	—
H	Fab U1 heavy chain	protein	223	8% helix, 51% strand	—
L	Fab U1 light chain	protein	211	6% helix, 53% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains E, H

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

Pockets

6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	691	0.65	0.75	61	empty
2	118	0.65	0.89	24	empty
3	136	0.46	0.77	27	empty
4	115	0.35	0.73	22	empty
5	73	0.31	0.74	13	empty

Interfaces

2 interfaces between chains.

H–L · 1931 Å² buried · 16 hydrogen bonds · protein-protein
E–H · 696 Å² buried · 9 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

6WO3 · Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to… · 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
Elsewhere: RCSB PDB 6WO3 · PDBe 6WO3

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