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Structure of the core ectodomain of the hepatitis C virus envelope glycoprotein 2 with tamarin CD81

Analyse Structure of the core ectodomain of the hepatitis C virus envelope glycoprotein… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7MWX
Type: protein
Length: 1,389 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Core protein precursor EE2; 2A12 Fab heavy chain; 2A12 Fab light chain; CD81 protein
EC: 2.7.7.48, 3.4.21.98, 3.6.1.15, 3.6.4.13
UniProt: A0A2I6PIY1, Q9N0J9
Ligands: NAG, BMA
Pockets: 16 · best druggability 0.78

Structure

x-ray diffraction · 6 distinct chains · 14% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	Core protein precursor EE2 (EC 2.7.7.48, 3.4.21.98, 3.6.1.15, 3.6.4.13)	protein	172	6% helix, 26% strand	A0A2I6PIY1
G	Core protein precursor EE2 (EC 2.7.7.48, 3.4.21.98, 3.6.1.15, 3.6.4.13)	protein	180	8% helix, 20% strand	A0A2I6PIY1
A, E	2A12 Fab heavy chain	protein	218	3% helix, 50% strand	—
B, F	2A12 Fab light chain	protein	218	7% helix, 53% strand	—
D	CD81 protein	protein	81	47% helix, 0% strand	Q9N0J9
H	CD81 protein	protein	84	54% helix, 0% strand	Q9N0J9

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains C, G
BMA · beta-D-mannopyranose · sugar

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

Pockets

16 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	371	0.78	0.87	51	empty
2	459	0.75	0.84	48	empty
3	868	0.73	0.77	93	empty
4	377	0.73	0.84	67	empty
5	381	0.64	0.78	58	empty

Interfaces

13 interfaces between chains.

A–B · 1908 Å² buried · 15 hydrogen bonds · protein-protein
E–F · 1806 Å² buried · 17 hydrogen bonds · protein-protein
G–H · 992 Å² buried · 7 hydrogen bonds · protein-protein
C–D · 900 Å² buried · 10 hydrogen bonds · protein-protein
G–E · 679 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 24 disulfide, 5 glycan (disulfide, N-glycosylation).

Compared structures

7MWX · Structure of the core ectodomain of the hepatitis C virus envelope glycoprotein 2 with… · the same entry in another collection · chain H against H, TM-score 1.00
Q9N0J9 · AlphaFold monomer V2.0 prediction for CD81 protein (Q9N0J9) · a predicted model of the same protein · chain H against A, TM-score 0.72

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 A0A2I6PIY1
Every structure of UniProt Q9N0J9
Elsewhere: RCSB PDB 7MWX · PDBe 7MWX · UniProt A0A2I6PIY1 · UniProt Q9N0J9

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