MolNFT v1 · #108674 · protein

Structure of the core ectodomain of the hepatitis C virus envelope glycoprotein 2

4WEB: “Structure of the core ectodomain of the hepatitis C virus envelope glycoprotein 2”. X-ray diffraction, 2 ligands (ARF, NAG), 7 pockets (best druggability 0.62). MolNFT v1 #108674 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4WEB
Type: protein
Length: 556 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Hepatitis C virus envelope glycoprotein 2; Mouse Fab heavy chain; Mouse Fab light chain
UniProt: Q9QF35
Ligands: ARF, NAG
Pockets: 7 · best druggability 0.62

Structure

x-ray diffraction · 3 distinct chains · 7% helix, 47% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
E	Hepatitis C virus envelope glycoprotein 2	protein	123	9% helix, 33% strand	Q9QF35
H	Mouse Fab heavy chain	protein	216	7% helix, 50% strand	—
L	Mouse Fab light chain	protein	217	6% helix, 51% strand	—

Ligands and binding sites

ARF · Formamide · ligand · 6 copies · chains E, H, L
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

7 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	534	0.62	0.75	60	ARF
2	54	0.45	0.85	20	empty
3	162	0.42	0.74	24	ARF
4	144	0.42	0.74	19	empty
5	130	0.42	0.75	21	ARF

Interfaces

3 interfaces between chains.

H–L · 1784 Å² buried · 17 hydrogen bonds · protein-protein
E–H · 495 Å² buried · 9 hydrogen bonds · protein-protein
E–L · 103 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 9 disulfide, 2 glycan (disulfide, N-glycosylation).

Compared structures

4WEB · Structure of the core ectodomain of the hepatitis C virus envelope glycoprotein 2 · 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 Q9QF35
Elsewhere: RCSB PDB 4WEB · PDBe 4WEB · UniProt Q9QF35

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