4WHT | pdb_00004wht

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

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
X [auth Y]	d4whty2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
X [auth Y]	d4whty1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
W [auth V]	d4whtv2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
W [auth V]	d4whtv1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
V [auth T]	d4whtt2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
V [auth T]	d4whtt1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
U [auth R]	d4whtr2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
U [auth R]	d4whtr1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
T [auth P]	d4whtp2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
T [auth P]	d4whtp1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
S [auth N]	d4whtn2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
S [auth N]	d4whtn1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
R [auth L]	d4whtl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
R [auth L]	d4whtl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
Q [auth H]	d4whth1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
P [auth F]	d4whtf1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
O [auth D]	d4whtd2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
O [auth D]	d4whtd1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
N [auth B]	d4whtb2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
N [auth B]	d4whtb1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)
F [auth J]	d4whtj1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	Norway rat (Rattus norvegicus ) [TaxId: 10116 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
X [auth Y]	Glyco_hydro_3	e4whtY1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
W [auth V]	Glyco_hydro_3	e4whtV1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
V [auth T]	Glyco_hydro_3	e4whtT1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
U [auth R]	Glyco_hydro_3	e4whtR1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
T [auth P]	Glyco_hydro_3	e4whtP1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
S [auth N]	Glyco_hydro_3	e4whtN1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
R [auth L]	Glyco_hydro_3	e4whtL1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
Q [auth H]	Glyco_hydro_3	e4whtH1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
P [auth F]	Glyco_hydro_3	e4whtF1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
O [auth D]	Glyco_hydro_3	e4whtD1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
N [auth B]	Glyco_hydro_3	e4whtB1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
F [auth J]	Glyco_hydro_3	e4whtJ1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
M [auth X]	Glyco_hydro_3	e4whtX1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
L [auth U]	Glyco_hydro_3	e4whtU1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
K [auth S]	Glyco_hydro_3	e4whtS1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
J [auth Q]	Glyco_hydro_3	e4whtQ1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
I [auth O]	Glyco_hydro_3	e4whtO1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
H [auth M]	Glyco_hydro_3	e4whtM1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
G [auth K]	Glyco_hydro_3	e4whtK1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
E [auth I]	Glyco_hydro_3	e4whtI1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
D [auth G]	Glyco_hydro_3	e4whtG1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
C [auth E]	Glyco_hydro_3	e4whtE1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
B [auth C]	Glyco_hydro_3	e4whtC1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)
A	Glyco_hydro_3	e4whtA1	A: a/b three-layered sandwiches	X: CCHC-type 1 zinc finger	H: Retrovirus zinc finger-related domains	T: Retrovirus zinc finger-related domains	F: Glyco_hydro_3	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
X [auth Y]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
W [auth V]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
V [auth T]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
U [auth R]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
T [auth P]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
S [auth N]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
R [auth L]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
Q [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
P [auth F]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
O [auth D]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
N [auth B]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
F [auth J]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
M [auth X]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
L [auth U]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K [auth S]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
J [auth Q]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
I [auth O]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
H [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
G [auth K]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
E [auth I]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
D [auth G]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth E]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B [auth C]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
A	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)

IMGT Antibody Annotation IMGT Database Homepage

Chain	Protein Name	Description	Organism Name	Gene Allele Name(s)	Domain Name(s)	Receptor Type	Receptor Description	Provenance Source
F [auth J], N [auth B], O [auth D], P [auth F], Q [auth H], F [auth J], N [auth B], O [auth D], P [auth F], Q [auth H], R [auth L], S [auth N], T [auth P], U [auth R], V [auth T], W [auth V], X [auth Y]	3/11 Fab, anti-hepatitis C virus (HCV) envelope glycoprotein E2,	L-KAPPA	Rattus norvegicus (Norway rat)	IGKV2S2501, IGKJ2-301, IGKJ2-101, IGKJ2-201, IGKC*01	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202614-0)
A, B [auth C], C [auth E], D [auth G], E [auth I], A, B [auth C], C [auth E], D [auth G], E [auth I], G [auth K], H [auth M], I [auth O], J [auth Q], K [auth S], L [auth U], M [auth X]	3/11 Fab, anti-hepatitis C virus (HCV) envelope glycoprotein E2,	VH-CH1	Rattus norvegicus (Norway rat)	IGHV5-2001, IGHJ201, IGHJ401, IGHG101	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202614-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
F [auth J], N [auth B], O [auth D], P [auth F], Q [auth H], F [auth J], N [auth B], O [auth D], P [auth F], Q [auth H], R [auth L], S [auth N], T [auth P], U [auth R], V [auth T], W [auth V], X [auth Y]	Light Chain	IGKV2	Kappa	-	SAbDab (2026-04-17)
A, B [auth C], C [auth E], D [auth G], E [auth I], A, B [auth C], C [auth E], D [auth G], E [auth I], G [auth K], H [auth M], I [auth O], J [auth Q], K [auth S], L [auth U], M [auth X]	Heavy Chain	IGHV5	-	-	SAbDab (2026-04-17)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
AA [auth e], BA [auth g], CA [auth i], DA [auth k], EA [auth m], AA [auth e], BA [auth g], CA [auth i], DA [auth k], EA [auth m], FA [auth o], GA [auth q], HA [auth s], IA [auth u], JA [auth x], Y [auth a], Z [auth c]	Epitope peptide	-	viral process fusion of virus membrane with host endosome membrane membrane fusion involved in viral entry into host cell virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral life cycle adhesion of symbiont to host biological process involved in interaction with host biological process involved in symbiotic interaction symbiont entry into host cell symbiont entry into host	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host cell lipid droplet host intracellular region other organism part host cell cytoplasm part host intracellular membrane-bounded organelle host cell endoplasmic reticulum host cell membrane host intracellular organelle host cell endomembrane system host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host cell lipid droplet host intracellular region other organism part host cell cytoplasm part host intracellular membrane-bounded organelle host cell endoplasmic reticulum host cell membrane host intracellular organelle host cell endomembrane system host cell endoplasmic reticulum membrane virion component viral membrane viral envelope virion membrane
F [auth J], N [auth B], O [auth D], P [auth F], Q [auth H], F [auth J], N [auth B], O [auth D], P [auth F], Q [auth H], R [auth L], S [auth N], T [auth P], U [auth R], V [auth T], W [auth V], X [auth Y]	Light chain of the Fab fragment derived from neutralizing antibody 3/11	-	-	-
A, B [auth C], C [auth E], D [auth G], E [auth I], A, B [auth C], C [auth E], D [auth G], E [auth I], G [auth K], H [auth M], I [auth O], J [auth Q], K [auth S], L [auth U], M [auth X]	Heavy chain of the Fab fragment derived from neutralizing antibody 3/11	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
AA [auth e], BA [auth g], CA [auth i], DA [auth k], EA [auth m], AA [auth e], BA [auth g], CA [auth i], DA [auth k], EA [auth m], FA [auth o], GA [auth q], HA [auth s], IA [auth u], JA [auth x], Y [auth a], Z [auth c]	IPR002519	Hepatitis C virus, Envelope glycoprotein E1	Domain
AA [auth e], BA [auth g], CA [auth i], DA [auth k], EA [auth m], AA [auth e], BA [auth g], CA [auth i], DA [auth k], EA [auth m], FA [auth o], GA [auth q], HA [auth s], IA [auth u], JA [auth x], Y [auth a], Z [auth c]	IPR002531	Hepatitis C virus, Non-structural protein E2/NS1	Domain