5Y9F | pdb_00005y9f

Crystal structure of HPV59 pentamer in complex with the Fab fragment of antibody 28F10

External Resource: Annotation

Domain Annotation: SCOP2 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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	Group I dsDNA viruses	8071422	3000939	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Group I dsDNA viruses	8071422	3000939	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Group I dsDNA viruses	8071422	3000939	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Group I dsDNA viruses	8071422	3000939	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Group I dsDNA viruses	8071422	3000939	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Group I dsDNA viruses	8071422	3000939	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Group I dsDNA viruses	8071422	3000939	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Group I dsDNA viruses	8071422	3000939	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Group I dsDNA viruses	8071422	3000939	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Group I dsDNA viruses	8071422	3000939	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Peptidase_S26	e5y9fA1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
B	Peptidase_S26	e5y9fB1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
C	Peptidase_S26	e5y9fC1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
D	Peptidase_S26	e5y9fD1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
E	Peptidase_S26	e5y9fE1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
F	Peptidase_S26	e5y9fF1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
G	Peptidase_S26	e5y9fG1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
H	Peptidase_S26	e5y9fH1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
I	Peptidase_S26	e5y9fI1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
J	Peptidase_S26	e5y9fJ1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
DA [auth U]	Peptidase_S26	e5y9fU1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
K	Peptidase_S26	e5y9fK1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
M [auth O]	Peptidase_S26	e5y9fO1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
O [auth Q]	Peptidase_S26	e5y9fQ1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
S [auth M]	Peptidase_S26	e5y9fM1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
U [auth c]	Peptidase_S26	e5y9fc1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
X [auth W]	Peptidase_S26	e5y9fW1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
Z [auth Y]	Peptidase_S26	e5y9fY1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
Q [auth S]	Peptidase_S26	e5y9fS1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
BA [auth a]	Peptidase_S26	e5y9fa1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
AA [auth Z]	Peptidase_S26	e5y9fZ1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
L	Peptidase_S26	e5y9fL1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
N [auth P]	Peptidase_S26	e5y9fP1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
P [auth R]	Peptidase_S26	e5y9fR1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
R [auth T]	Peptidase_S26	e5y9fT1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
T [auth N]	Peptidase_S26	e5y9fN1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
V [auth d]	Peptidase_S26	e5y9fd1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
W [auth V]	Peptidase_S26	e5y9fV1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
Y [auth X]	Peptidase_S26	e5y9fX1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)
CA [auth b]	Peptidase_S26	e5y9fb1	A: alpha bundles	X: TIM beta/alpha-barrel	H: TIM barrels	T: TIM barrels	F: Peptidase_S26	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.60.175.20	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
B	2.60.175.20	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
C	2.60.175.20	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
D	2.60.175.20	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
E	2.60.175.20	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
F	2.60.175.20	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
G	2.60.175.20	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
H	2.60.175.20	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
I	2.60.175.20	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
J	2.60.175.20	Mainly Beta	Sandwich	Polyomavirus Vp1	Chain A	CATH (4.3.0)
DA [auth U]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
K	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
M [auth O]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
O [auth Q]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
S [auth M]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
U [auth c]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
X [auth W]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
Z [auth Y]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
Q [auth S]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
BA [auth a]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
AA [auth Z]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
L	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
N [auth P]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
P [auth R]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
R [auth T]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
T [auth N]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
V [auth d]	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)
Y [auth X]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
CA [auth b]	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
BA [auth a], DA [auth U], K, M [auth O], O [auth Q], BA [auth a], DA [auth U], K, M [auth O], O [auth Q], Q [auth S], S [auth M], U [auth c], X [auth W], Z [auth Y]	Fab 28F10	L-KAPPA	Mus musculus (house mouse)	IGKV1-11001, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-2C_KAPPA	IMGT (202610-0)
AA [auth Z], CA [auth b], L, N [auth P], P [auth R], AA [auth Z], CA [auth b], L, N [auth P], P [auth R], R [auth T], T [auth N], V [auth d], W [auth V], Y [auth X]	Fab 28F10	VH-CH1	Mus musculus (house mouse)	IGHV5-6-401, IGHJ401, IGHG2C01, IGHG2C02, IGHG2C*03	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-2C_KAPPA	IMGT (202610-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
BA [auth a], DA [auth U], K, M [auth O], O [auth Q], BA [auth a], DA [auth U], K, M [auth O], O [auth Q], Q [auth S], S [auth M], U [auth c], X [auth W], Z [auth Y]	Light Chain	IGKV1	Kappa	light chains of fab fragment of antibody 28f10, heavy chain of fab fragment of antibody 28f10, major capsid protein l1	SAbDab (2026-03-20)
AA [auth Z], CA [auth b], L, N [auth P], P [auth R], AA [auth Z], CA [auth b], L, N [auth P], P [auth R], R [auth T], T [auth N], V [auth d], W [auth V], Y [auth X]	Heavy Chain	IGHV5	-	light chains of fab fragment of antibody 28f10, heavy chain of fab fragment of antibody 28f10, major capsid protein l1	SAbDab (2026-03-20)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	Major capsid protein L1	structural molecule activity	virion attachment to host cell biological process involved in interspecies interaction between organisms adhesion of symbiont to host cell viral process 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 endocytosis involved in viral entry into host cell	viral capsid icosahedral viral capsid T=7 icosahedral viral capsid virion component host intracellular membrane-bounded organelle host cellular component host intracellular part cellular anatomical structure host cell part host intracellular region host cell nucleus other organism part host intracellular organelle
BA [auth a], DA [auth U], K, M [auth O], O [auth Q], BA [auth a], DA [auth U], K, M [auth O], O [auth Q], Q [auth S], S [auth M], U [auth c], X [auth W], Z [auth Y]	light chains of Fab fragment of antibody 28F10	-	-	-
AA [auth Z], CA [auth b], L, N [auth P], P [auth R], AA [auth Z], CA [auth b], L, N [auth P], P [auth R], R [auth T], T [auth N], V [auth d], W [auth V], Y [auth X]	heavy chain of Fab fragment of antibody 28F10	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR036973	Major capsid L1 (late) superfamily, Papillomavirus	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR011222	Double-stranded DNA virus, group I, capsid	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J	IPR002210	Major capsid L1 (late) protein, Papillomavirus	Family