1QGC | pdb_00001qgc

STRUCTURE OF THE COMPLEX OF A FAB FRAGMENT OF A NEUTRALIZING ANTIBODY WITH FOOT AND MOUTH DISEASE VIRUS

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
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)
F [auth 5]	d1qgc5_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	FMDV complexed with a neutralizing Fab fragment	(Foot and mouth disease virus C ) [TaxId: 12116 ],	SCOPe (2.08)
D [auth 4]	d1qgc4_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	FMDV complexed with a neutralizing Fab fragment	(Mus musculus ) [TaxId: 10090 ],	SCOPe (2.08)
C [auth 3]	d1qgc3_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	FMDV complexed with a neutralizing Fab fragment	(Foot and mouth disease virus C ) [TaxId: 12116 ],	SCOPe (2.08)
B [auth 2]	d1qgc2_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	FMDV complexed with a neutralizing Fab fragment	(Foot and mouth disease virus C ) [TaxId: 12116 ],	SCOPe (2.08)
A [auth 1]	d1qgc1_	Low resolution protein structures	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	Viruses and virus-receptor complexes	FMDV complexed with a neutralizing Fab fragment	(Foot and mouth disease virus C ) [TaxId: 12116 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
C [auth 3]	SCOP2 Family	Picornaviridae-like VP (VP1, VP2, VP3 and VP4)	8068077	4003466	SCOP2 (2022-06-29)
C [auth 3]	SCOP2 Superfamily	Positive stranded ssRNA viruses-like	8068078	3000918	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)
E [auth A]		e1qgcA01	A: alpha arrays	X: RNase A-like	H: RNase A-like	T: RNase A-like	F:	ECOD (v295.2)
D [auth 4]	TAFII55_N	e1qgc41	A: alpha arrays	X: HTH	H: HTH	T: Three-helical HTH	F: TAFII55_N	ECOD (v295.2)
C [auth 3]	DUF1684	e1qgc31	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: DUF1684	ECOD (v295.2)
B [auth 2]	DUF1684	e1qgc21	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: DUF1684	ECOD (v295.2)
A [auth 1]	DUF1684	e1qgc11	A: alpha arrays	X: Alpha-beta plaits	H: Phage tail protein-like	T: Transmembrane protein 14A	F: DUF1684	ECOD (v295.2)

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
E [auth A]	Fab fragment neutralizing foot-and-mouth disease virus	VH-CH1	Mus musculus (house mouse)	IGHV5-9-101, IGHJ301, IGHG1*02	V-DOMAIN VH, C-DOMAIN CH1	IG	FAB-GAMMA-1_KAPPA	IMGT (202640-0)
D [auth 4]	Fab fragment neutralizing foot-and-mouth disease virus	L-KAPPA	Mus musculus (house mouse)	IGKV3-501, IGKJ501, IGKC01, IGKC02	V-DOMAIN V-KAPPA, C-DOMAIN C-KAPPA	IG	FAB-GAMMA-1_KAPPA	IMGT (202640-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth A]	Heavy Chain	IGHV5	-	protein (gh-loop from virus capsid protein vp1) \| protein (virus capsid protein vp1) \| protein (virus capsid protein vp3)	SAbDab (2026-10-16)
D [auth 4]	Light Chain	IGKV3	Kappa	protein (gh-loop from virus capsid protein vp1) \| protein (virus capsid protein vp1) \| protein (virus capsid protein vp3)	SAbDab (2026-10-16)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
D [auth 4]	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
F [auth 5]	PROTEIN (GH-LOOP FROM VIRUS CAPSID PROTEIN VP1)	-	-	-
E [auth A]	PROTEIN (IMMUNOGLOBULIN HEAVY CHAIN)	-	-	-
D [auth 4]	PROTEIN (IMMUNOGLOBULIN LIGHT CHAIN)	-	-	-
C [auth 3]	PROTEIN (VIRUS CAPSID PROTEIN VP3)	cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity cysteine-type peptidase activity peptidase activity catalytic activity, acting on a protein cysteine-type endopeptidase activity hydrolase activity catalytic activity endopeptidase activity RNA-directed RNA polymerase activity 5'-3' RNA polymerase activity catalytic activity, acting on RNA catalytic activity, acting on a nucleic acid RNA polymerase activity transferase activity nucleotidyltransferase activity transferase activity, transferring phosphorus-containing groups RNA binding binding nucleic acid binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding pyrophosphatase activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity, acting on acid anhydrides passive transmembrane transporter activity channel activity transporter activity transmembrane transporter activity nucleic acid conformation isomerase activity isomerase activity helicase activity RNA helicase activity ATP-dependent activity, acting on RNA macromolecular conformation isomerase activity ATP-dependent activity structural molecule activity	RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process RNA metabolic process viral life cycle primary metabolic process nucleobase-containing compound biosynthetic process macromolecule biosynthetic process nucleic acid metabolic process RNA biosynthetic process nucleobase-containing compound metabolic process nucleic acid biosynthetic process viral genome replication biosynthetic process viral RNA genome replication viral process metabolic process cellular process macromolecule metabolic process symbiont-mediated perturbation of host cellular process biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host process modulation of process of another organism biological process involved in interaction with host symbiont-mediated perturbation of host chromatin organization biological process involved in symbiotic interaction import into cell receptor-mediated endocytosis of virus by host cell transport establishment of localization vesicle-mediated transport localization symbiont entry into host cell clathrin-dependent endocytosis symbiont entry into host clathrin-dependent endocytosis of virus by host cell receptor-mediated endocytosis endocytosis endocytosis involved in viral entry into host cell transmembrane transport monoatomic ion transmembrane transport monoatomic ion transport viral gene expression viral protein processing gene expression DNA-templated transcription virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host symbiont-mediated perturbation of host autophagy symbiont-mediated activation of host autophagy proteolysis protein metabolic process	host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part host intracellular membrane-bounded organelle host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle viral capsid host cellular component host intracellular part cellular anatomical structure host cell cytoplasm host cell part host intracellular region other organism part host intracellular membrane-bounded organelle host cell membrane host cell cytoplasmic vesicle membrane host cell cytoplasm part host intracellular organelle host cell cytoplasmic vesicle viral capsid icosahedral viral capsid virion component T=pseudo3 icosahedral viral capsid host cell endoplasmic reticulum host cell endomembrane system host cell endoplasmic reticulum membrane host cell nucleus
B [auth 2]	PROTEIN (VIRUS CAPSID PROTEIN VP2)	-	-	-
A [auth 1]	PROTEIN (VIRUS CAPSID PROTEIN VP1)	-	-	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
C [auth 3]	IPR001205	RNA-directed RNA polymerase, C-terminal domain	Domain
C [auth 3]	IPR043128	Reverse transcriptase/Diguanylate cyclase domain	Homologous Superfamily
C [auth 3]	IPR038765	Papain-like cysteine peptidase superfamily	Homologous Superfamily
C [auth 3]	IPR008739	Peptidase C28, foot-and-mouth virus L-proteinase	Domain
C [auth 3]	IPR000199	Peptidase C3A/C3B, picornaviral	Domain
C [auth 3]	IPR001676	Picornavirus capsid	Domain
C [auth 3]	IPR014759	Helicase, superfamily 3, single-stranded RNA virus	Domain
C [auth 3]	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
C [auth 3]	IPR029053	Viral coat protein subunit	Homologous Superfamily
C [auth 3]	IPR004080	Foot-and-mouth disease virus VP1 coat	Domain
C [auth 3]	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
C [auth 3]	IPR004004	Helicase/polymerase/peptidase polyprotein, Calicivirus-type	Family
C [auth 3]	IPR043502	DNA/RNA polymerase superfamily	Homologous Superfamily
C [auth 3]	IPR044067	Picornavirales 3C/3C-like protease domain	Domain
C [auth 3]	IPR033703	Picornavirus/Calicivirus coat protein	Domain
C [auth 3]	IPR007094	RNA-directed RNA polymerase, catalytic domain	Domain
C [auth 3]	IPR000605	Helicase, superfamily 3, single-stranded DNA/RNA virus	Domain
C [auth 3]	IPR037080	Capsid protein VP4 superfamily, Picornavirus	Homologous Superfamily

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
D [auth 4]	OCS	Parent Component: CYS : AA0556 : L-cysteic acid (L-cysteine sulfonic acid) MOD:00460