4EJ1 | pdb_00004ej1

Binding of Nb113 camelid antibody fragment with the binary DHFR:folate 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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
D	d4ej1d1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
D	d4ej1d2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d4ej1c1	All beta proteins	Immunoglobulin-like beta-sandwich	Immunoglobulin	V set domains (antibody variable domain-like)	automated matches	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
C	d4ej1c2	Artifacts	Tags	Tags	Tags	C-terminal Tags	(Lama glama ) [TaxId: 9844 ],	SCOPe (2.08)
B	d4ej1b_	Alpha and beta proteins (a/b)	Dihydrofolate reductase-like	Dihydrofolate reductase-like	Dihydrofolate reductases	Dihydrofolate reductase, prokaryotic type	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
A	d4ej1a_	Alpha and beta proteins (a/b)	Dihydrofolate reductase-like	Dihydrofolate reductase-like	Dihydrofolate reductases	Dihydrofolate reductase, prokaryotic type	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	Dihydrofolate reductase-like	8032695	3001255	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Dihydrofolate reductase-like	8032695	3001255	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)
D	V-set_8	e4ej1D1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
C	V-set_8	e4ej1C1	A: beta sandwiches	X: Immunoglobulin-like beta-sandwich	H: Immunoglobulin-related	T: Immunoglobulin/Fibronectin type III/E set domains/PapD-like	F: V-set_8	ECOD (1.6)
B	DHFR_1	e4ej1B1	A: a/b three-layered sandwiches	X: Dihydrofolate reductases (From Topology)	H: Dihydrofolate reductases (From Topology)	T: Dihydrofolate reductases	F: DHFR_1	ECOD (1.6)
A	DHFR_1	e4ej1A1	A: a/b three-layered sandwiches	X: Dihydrofolate reductases (From Topology)	H: Dihydrofolate reductases (From Topology)	T: Dihydrofolate reductases	F: DHFR_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
C	2.60.40.10	Mainly Beta	Sandwich	Immunoglobulin-like	Immunoglobulins	CATH (4.3.0)
B	3.40.430.10	Alpha Beta	3-Layer(aba) Sandwich	Dihydrofolate Reductase, subunit A	Dihydrofolate Reductase, subunit A	CATH (4.3.0)
A	3.40.430.10	Alpha Beta	3-Layer(aba) Sandwich	Dihydrofolate Reductase, subunit A	Dihydrofolate Reductase, subunit A	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
C, D	Nb113	VH	Lama glama (llama)	IGHV3S301, IGHJ601	V-DOMAIN VH	IG	(VH)	IMGT (202542-0)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
C, D	Heavy Chain	IGHV1	-	dihydrofolate reductase	SAbDab (2025-10-31)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00186	Dihydrofolate reductase (DHFR_1)	Dihydrofolate reductase		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
C, D	Nb113 camelid antibody fragment	-	-	-
A, B	Dihydrofolate reductase	amide binding organic acid binding binding ion binding anion binding carboxylic acid binding heterocyclic compound binding methotrexate binding small molecule binding NADP+ binding nucleotide binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding amide binding organic acid binding binding ion binding anion binding carboxylic acid binding heterocyclic compound binding methotrexate binding small molecule binding NADP+ binding nucleotide binding nucleoside phosphate binding purine nucleotide binding adenyl nucleotide binding NADP binding dihydrofolic acid binding modified amino acid binding NADPH binding vitamin binding folic acid binding dihydrofolate reductase activity oxidoreductase activity oxidoreductase activity, acting on the CH-NH group of donors, NAD or NADP as acceptor oxidoreductase activity, acting on the CH-NH group of donors catalytic activity	response to stimulus response to chemical response to xenobiotic stimulus response to methotrexate response to oxygen-containing compound response to nitrogen compound small molecule metabolic process metabolic process cellular process one-carbon metabolic process oxoacid metabolic process dicarboxylic acid metabolic process dihydrofolate metabolic process carboxylic acid metabolic process response to stimulus response to chemical response to xenobiotic stimulus response to methotrexate response to oxygen-containing compound response to nitrogen compound small molecule metabolic process metabolic process cellular process one-carbon metabolic process oxoacid metabolic process dicarboxylic acid metabolic process dihydrofolate metabolic process carboxylic acid metabolic process modified amino acid metabolic process organic acid metabolic process folic acid-containing compound metabolic process pteridine-containing compound metabolic process amide metabolic process folic acid metabolic process response to antibiotic modified amino acid biosynthetic process vitamin biosynthetic process organic acid biosynthetic process carboxylic acid biosynthetic process dicarboxylic acid biosynthetic process folic acid biosynthetic process folic acid-containing compound biosynthetic process water-soluble vitamin biosynthetic process small molecule biosynthetic process amide biosynthetic process vitamin metabolic process biosynthetic process pteridine-containing compound biosynthetic process tetrahydrofolate biosynthetic process tetrahydrofolate metabolic process 10-formyltetrahydrofolate metabolic process 10-formyltetrahydrofolate biosynthetic process	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR017925	Dihydrofolate reductase conserved site	Conserved Site
A, B	IPR012259	Dihydrofolate reductase	Family
A, B	IPR024072	Dihydrofolate reductase-like domain superfamily	Homologous Superfamily
A, B	IPR001796	Dihydrofolate reductase domain	Domain

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), 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 R01GM157729.