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Structure of hepatitis C virus envelope glycoprotein E2 core from genotype 6A bound to broadly neutralizing antibody AR3B

Analyse Structure of hepatitis C virus envelope glycoprotein E2 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: 6BKC
Type: protein
Length: 576 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab AR3B heavy chain; Fab AR3B light chain; Polyprotein
UniProt: P0DOX5, Q8TCD0, B9V0E2
Ligands: NAG
Pockets: 2 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab AR3B heavy chain	protein	219	3% helix, 53% strand	P0DOX5
L	Fab AR3B light chain	protein	214	6% helix, 54% strand	Q8TCD0
E	Polyprotein	protein	143	13% helix, 38% strand	B9V0E2

Ligands and binding sites

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

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	355	0.56	0.75	51	empty
2	117	0.41	0.76	22	empty

Interfaces

3 interfaces between chains.

H–L · 1729 Å² buried · 11 hydrogen bonds · protein-protein
H–E · 792 Å² buried · 10 hydrogen bonds · protein-protein
L–E · 40 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

6BKC · Structure of Hepatitis C Virus Envelope Glycoprotein E2 core from genotype 6a bound to… · the same entry in another collection · chain H against H, 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 P0DOX5
Every structure of UniProt Q8TCD0
Every structure of UniProt B9V0E2
Elsewhere: RCSB PDB 6BKC · PDBe 6BKC · UniProt P0DOX5 · UniProt Q8TCD0 · UniProt B9V0E2

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