2J4W

Structure of a Plasmodium vivax apical membrane antigen 1-Fab F8.12.19 complex

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
IMGT Antibody Annotation
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A [auth D]	d2j4wd1	Small proteins	Apical membrane antigen 1	Apical membrane antigen 1	Apical membrane antigen 1	Apical membrane antigen 1	(Plasmodium vivax ) [TaxId: 5855 ],	SCOPe (2.08)
B [auth H]	d2j4wh1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	Immunoglobulin heavy chain variable domain, VH	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
B [auth H]	d2j4wh2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d2j4wl2	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	C1 set domains (antibody constant domain-like)	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth L]	d2j4wl1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	automated matches	automated matches	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth D]	SCOP2 Family	Apical membrane antigen 1	8020873	4003417	SCOP2 (2022-06-29)
A [auth D]	SCOP2 Superfamily	Apical membrane antigen 1	8033253	3000822	SCOP2 (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 [auth D]	PF02430	e2j4wD1	A: few secondary structure elements	X: Apical membrane antigen 1 (From Topology)	H: Apical membrane antigen 1 (From Topology)	T: Apical membrane antigen 1	F: PF02430	ECOD (1.6)
B [auth H]	PF07654	e2j4wH2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
B [auth H]	PF07686	e2j4wH1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)
C [auth L]	PF07654	e2j4wL2	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07654	ECOD (1.6)
C [auth L]	PF07686	e2j4wL1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: PF07686	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B [auth H]	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C [auth L]	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
B [auth H]	F8.12.19	VH-CH1	Mus musculus (house mouse)	IGHV5-402, IGHJ301, IGHG1*01	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)
C [auth L]	F8.12.19	L-KAPPA	Mus musculus (house mouse)	IGKV4-7201, IGKJ203, IGKJ401, IGKC01, IGKC*02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202416-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
B [auth H]	Heavy Chain	IGHV5	-	apical membrane antigen 1	SAbDab (2024-04-26)
C [auth L]	Light Chain	IGKV4	Kappa	apical membrane antigen 1	SAbDab (2024-04-26)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth D]	PF02430	Apical membrane antigen 1 (AMA-1)	Apical membrane antigen 1	-	Family
B [auth H]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
B [auth H]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain
C [auth L]	PF07686	Immunoglobulin V-set domain (V-set)	Immunoglobulin V-set domain	This domain is found in antibodies as well as neural protein P0 and CTL4 amongst others.	Domain
C [auth L]	PF07654	Immunoglobulin C1-set domain (C1-set)	Immunoglobulin C1-set domain	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth D]	APICAL MEMBRANE ANTIGEN 1	-	-	membrane cellular anatomical entity
B [auth H]	FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19	-	-	-
C [auth L]	FAB FRAGMENT OF MONOCLONAL ANTIBODY F8.12.19	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth D]	IPR024056	Apical membrane antigen 1 domain superfamily	Homologous Superfamily
A [auth D]	IPR003298	Apical membrane antigen 1	Family
B [auth H]	IPR003597	Immunoglobulin C1-set	Domain
B [auth H]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
B [auth H]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
B [auth H]	IPR003599	Immunoglobulin subtype	Domain
B [auth H]	IPR013106	Immunoglobulin V-set domain	Domain
B [auth H]	IPR007110	Immunoglobulin-like domain	Domain
C [auth L]	IPR003597	Immunoglobulin C1-set	Domain
C [auth L]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
C [auth L]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
C [auth L]	IPR003599	Immunoglobulin subtype	Domain
C [auth L]	IPR013106	Immunoglobulin V-set domain	Domain
C [auth L]	IPR007110	Immunoglobulin-like domain	Domain
C [auth L]	IPR003006	Immunoglobulin/major histocompatibility complex, conserved site	Conserved Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
C [auth L]	PCA	Parent Component: GLN RESID: AA0031 PSI-MOD : 2-pyrrolidone-5-carboxylic acid (Gln) MOD:00040 , 2-pyrrolidone-5-carboxylic acid (Glu) MOD:00420

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM133198.