MolNFT v1 · #100402 · protein

Structure of hepatitis C virus envelope glycoprotein E2 core bound to broadly neutralizing antibody AR3C

4MWF · Fab AR3C heavy chain: “Structure of hepatitis C virus envelope glycoprotein E2 core bound to broadly neutralizing antibody AR3C”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 14 pockets (best druggability 0.72). MolNFT v1 #100402…

PDB: 4MWF
Type: protein
Length: 1,214 residues
Chains: 6
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fab AR3C heavy chain; Fab AR3C light chain; Envelope glycoprotein E2
UniProt: P27958
Ligands: NAG, MAN, BMA
Pockets: 14 · best druggability 0.72

Structure

x-ray diffraction · 6 distinct chains · 8% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Fab AR3C heavy chain	protein	223	5% helix, 51% strand	—
B	Fab AR3C light chain	protein	211	5% helix, 51% strand	—
C	Envelope glycoprotein E2	protein	169	12% helix, 33% strand	P27958
D	Envelope glycoprotein E2	protein	171	12% helix, 31% strand	P27958
H	Fab AR3C heavy chain	protein	228	7% helix, 50% strand	—
L	Fab AR3C light chain	protein	212	7% helix, 50% strand	—

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 13 copies · chains C, H, L, D, A, B
MAN · alpha-D-mannopyranose · sugar · 5 copies
BMA · beta-D-mannopyranose · sugar

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

Pockets

14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	1034	0.72	0.76	117	empty
2	912	0.69	0.75	86	empty
3	243	0.51	0.75	32	empty
4	85	0.46	0.81	28	empty
5	159	0.43	0.75	29	empty

Interfaces

10 interfaces between chains.

H–L · 1764 Å² buried · 9 hydrogen bonds · protein-protein
A–B · 1676 Å² buried · 7 hydrogen bonds · protein-protein
C–H · 713 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 694 Å² buried · 7 hydrogen bonds · protein-protein
A–C · 520 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 22 disulfide, 10 glycan (disulfide, N-glycosylation).

Compared structures

4MWF · Structure of Hepatitis C Virus Envelope Glycoprotein E2 core bound to broadly… · the same entry in another collection · chain A against A, 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 P27958
Elsewhere: RCSB PDB 4MWF · PDBe 4MWF · UniProt P27958

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