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Structure of hepatitis C virus envelope glycoprotein E2C3 core from genotype 6A bound to broadly neutralizing antibody AR3A and non neutralizing antibody E1

Analyse Structure of hepatitis C virus envelope glycoprotein E2C3 core from genotype 6A… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6UYG
Type: protein
Length: 1,001 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Envelope glycoprotein E2; Fab AR3A heavy chain; Fab AR3A light chain; Fab E1 heavy chain…
UniProt: P19909
Ligands: NAG
Pockets: 12 · best druggability 0.63

Structure

x-ray diffraction · 6 distinct chains · 5% helix, 44% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Envelope glycoprotein E2	protein	146	10% helix, 34% strand	—
H	Fab AR3A heavy chain	protein	204	3% helix, 43% strand	—
L	Fab AR3A light chain	protein	190	4% helix, 42% strand	—
A	Fab E1 heavy chain	protein	195	2% helix, 48% strand	—
B	Fab E1 light chain	protein	209	4% helix, 47% strand	—
G	Immunoglobulin G-binding protein G	protein	57	21% helix, 47% strand	P19909

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains E, H, L

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

Pockets

12 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	631	0.63	0.74	61	empty
2	429	0.57	0.74	51	empty
3	71	0.57	0.88	20	empty
4	57	0.53	0.88	19	empty
5	99	0.44	0.78	19	empty

Interfaces

8 interfaces between chains.

A–B · 1655 Å² buried · 12 hydrogen bonds · protein-protein
H–L · 1653 Å² buried · 12 hydrogen bonds · protein-protein
E–H · 761 Å² buried · 8 hydrogen bonds · protein-protein
E–A · 752 Å² buried · 5 hydrogen bonds · protein-protein
H–G · 537 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 disulfide, 3 glycan (disulfide, N-glycosylation).

Compared structures

6UYG · Structure of Hepatitis C Virus Envelope Glycoprotein E2c3 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
Every structure of UniProt P19909
Elsewhere: RCSB PDB 6UYG · PDBe 6UYG · UniProt P19909

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