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Structure of hepatitis C virus envelope glycoprotein E2 core from genotype 6A bound to broadly neutralizing antibody AR3D

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: 6BKD
Type: protein
Length: 580 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Polyprotein; Fab AR3D heavy chain; Fab AR3D light chain
UniProt: B9V0E2, S6B2A6, Q6PIL8
Ligands: NAG
Pockets: 3 · best druggability 0.59

Structure

x-ray diffraction · 3 distinct chains · 6% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Polyprotein	protein	150	13% helix, 34% strand	B9V0E2
H	Fab AR3D heavy chain	protein	223	2% helix, 49% strand	S6B2A6
L	Fab AR3D light chain	protein	207	4% helix, 47% strand	Q6PIL8

Ligands and binding sites

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

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

Pockets

3 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	544	0.59	0.73	63	empty
2	121	0.40	0.75	23	empty
3	66	0.34	0.76	17	empty

Interfaces

2 interfaces between chains.

H–L · 1702 Å² buried · 9 hydrogen bonds · protein-protein
E–H · 693 Å² buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 8 disulfide, 1 glycan (disulfide, N-glycosylation).

Compared structures

6BKD · 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
Every structure of UniProt B9V0E2
Every structure of UniProt S6B2A6
Every structure of UniProt Q6PIL8
Elsewhere: RCSB PDB 6BKD · PDBe 6BKD · UniProt B9V0E2 · UniProt S6B2A6 · UniProt Q6PIL8

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