MolNFT v1 · #108777 · protein

Structure of the hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly neutralizing antibody 3/11, P1 crystal form

4WHT · Heavy chain of the Fab fragment derived from neutralizing…: “Structure of the hepatitis C virus envelope glycoprotein E2 antigenic region 412-423 bound to the broadly…”. X-ray diffraction, 20 pockets (best druggability 0.82). MolNFT…

PDB: 4WHT
Type: protein
Length: 5,168 residues
Chains: 36
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Heavy chain of the Fab fragment derived from neutralizing antibody 3/11; Light chain of…
UniProt: Q9WJJ4
Pockets: 20 · best druggability 0.82

Structure

x-ray diffraction · 18 distinct chains · 6% helix, 50% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Heavy chain of the Fab fragment derived from neutralizing antibody 3/11	protein	207	6% helix, 51% strand	—
C	Heavy chain of the Fab fragment derived from neutralizing antibody 3/11	protein	205	7% helix, 52% strand	—
E	Heavy chain of the Fab fragment derived from neutralizing antibody 3/11	protein	208	7% helix, 51% strand	—
G	Heavy chain of the Fab fragment derived from neutralizing antibody 3/11	protein	207	7% helix, 53% strand	—
I, O	Heavy chain of the Fab fragment derived from neutralizing antibody 3/11	protein	205	7% helix, 52% strand	—
J, B, F, L, N, P, R, T	Light chain of the Fab fragment derived from neutralizing antibody 3/11	protein	215	6% helix, 50% strand	—
K, M, S	Heavy chain of the Fab fragment derived from neutralizing antibody 3/11	protein	204	7% helix, 51% strand	—
Q	Heavy chain of the Fab fragment derived from neutralizing antibody 3/11	protein	206	7% helix, 52% strand	—
U	Heavy chain of the Fab fragment derived from neutralizing antibody 3/11	protein	205	6% helix, 52% strand	—
X	Heavy chain of the Fab fragment derived from neutralizing antibody 3/11	protein	199	9% helix, 54% strand	—
D	Light chain of the Fab fragment derived from neutralizing antibody 3/11	protein	216	6% helix, 51% strand	—
H	Light chain of the Fab fragment derived from neutralizing antibody 3/11	protein	216	6% helix, 50% strand	—
V	Light chain of the Fab fragment derived from neutralizing antibody 3/11	protein	212	6% helix, 50% strand	—
Y	Light chain of the Fab fragment derived from neutralizing antibody 3/11	protein	210	0% helix, 49% strand	—
a, g, i, m, x	Epitope peptide	protein	12	0% helix, 8% strand	Q9WJJ4
c, e, k, s	Epitope peptide	protein	11	0% helix, 0% strand	Q9WJJ4
o	Epitope peptide	protein	11	0% helix, 9% strand	Q9WJJ4
q, u	Epitope peptide	protein	10	0% helix, 0% strand	Q9WJJ4

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	830	0.82	0.84	96	empty
2	1182	0.70	0.75	127	empty
3	483	0.70	0.80	75	empty
4	499	0.70	0.80	78	empty
5	429	0.69	0.81	80	empty

Interfaces

79 interfaces between chains.

E–F · 1619 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1592 Å² buried · 15 hydrogen bonds · protein-protein
Q–R · 1585 Å² buried · 13 hydrogen bonds · protein-protein
K–L · 1577 Å² buried · 15 hydrogen bonds · protein-protein
U–V · 1569 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 48 disulfide (disulfide).

Compared structures

4WHT · Structure of the Hepatitis C virus envelope glycoprotein E2 antigenic region 412-423… · the same entry in another collection · chain C against C, 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 Q9WJJ4
Elsewhere: RCSB PDB 4WHT · PDBe 4WHT · UniProt Q9WJJ4

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