MolNFT v1 · #168685 · protein

Structure of hepatitis C virus envelope glycoprotein E2 core from genotype 6A bound to broadly neutralizing antibody HC11

6WO4 · Fab HC11 heavy chain: “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 0.60). MolNFT v1 #168685 on…

PDB: 6WO4
Type: protein
Length: 605 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab HC11 heavy chain; Envelope glycoprotein E2; Fab HC11 light chain
Ligands: NAG
Pockets: 6 · best druggability 0.60

Structure

x-ray diffraction · 3 distinct chains · 9% helix, 48% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
H	Fab HC11 heavy chain	protein	228	8% helix, 54% strand	—
E	Envelope glycoprotein E2	protein	163	12% helix, 35% strand	—
L	Fab HC11 light chain	protein	214	7% helix, 53% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains H, E, L

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	449	0.60	0.75	43	empty
2	216	0.52	0.76	45	empty
3	96	0.42	0.78	21	empty
4	84	0.38	0.77	26	empty
5	112	0.38	0.74	21	empty

Interfaces

3 interfaces between chains.

H–L · 1818 Å² buried · 14 hydrogen bonds · protein-protein
H–E · 685 Å² buried · 11 hydrogen bonds · protein-protein
E–L · 179 Å² buried · 2 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 11 disulfide, 4 glycan (disulfide, N-glycosylation).

Compared structures

6WO4 · 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
Elsewhere: RCSB PDB 6WO4 · PDBe 6WO4

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