7DF1

Crystal structure of human CD98 heavy chain extracellular domain in complex with S1-F4 scFv

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
SAbDab Antibody Annotation
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
B	SCOP2B Superfamily	(Trans)glycosidases	8052501	3000313	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8052503	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8052503	3001528	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	(Trans)glycosidases	8052501	3000313	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8052503	3001528	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	(Trans)glycosidases	8052501	3000313	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Glycosyl hydrolase domain-like	8052503	3001528	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	(Trans)glycosidases	8052501	3000313	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)
B	F_UNCLASSIFIED	e7df1B1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: F_UNCLASSIFIED	ECOD (1.6)
B	PF00128	e7df1B2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00128	ECOD (1.6)
C	F_UNCLASSIFIED	e7df1C1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: F_UNCLASSIFIED	ECOD (1.6)
C	PF00128	e7df1C2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00128	ECOD (1.6)
D	F_UNCLASSIFIED	e7df1D2	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: F_UNCLASSIFIED	ECOD (1.6)
D	PF00128	e7df1D1	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00128	ECOD (1.6)
A	F_UNCLASSIFIED	e7df1A1	A: beta sandwiches	X: Glycosyl hydrolase domain-like	H: Glycosyl hydrolase domain (From Topology)	T: Glycosyl hydrolase domain	F: F_UNCLASSIFIED	ECOD (1.6)
A	PF00128	e7df1A2	A: a/b barrels	X: TIM beta/alpha-barrel	H: TIM barrels (From Topology)	T: TIM barrels	F: PF00128	ECOD (1.6)
G [auth E]	PF07686	e7df1E1	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)
I [auth F]	PF07686	e7df1F1	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)
K [auth G]	PF07686	e7df1G1	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)
E [auth H]	PF07686	e7df1H1	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)
F [auth L]	PF07686	e7df1L1	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)
H [auth I]	PF07686	e7df1I1	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)
J	PF07686	e7df1J1	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)
L [auth K]	PF07686	e7df1K1	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)

SAbDab Antibody Annotation SAbDab Database Homepage

Chain	Chain Class	Chain Subclass	Chain Type	Antigen Name(s)	Provenance Source
E [auth H], G [auth E], I [auth F], K [auth G]	Heavy Chain	IGHV1	-	4f2 cell-surface antigen heavy chain	SAbDab (2024-05-03)
F [auth L], H [auth I], J, L [auth K]	Light Chain	IGKV4	Kappa	4f2 cell-surface antigen heavy chain	SAbDab (2024-05-03)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00128	Alpha amylase, catalytic domain (Alpha-amylase)	Alpha amylase, catalytic domain	Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, a ...	Alpha amylase is classified as family 13 of the glycosyl hydrolases. The structure is an 8 stranded alpha/beta barrel containing the active site, interrupted by a ~70 a.a. calcium-binding domain protruding between beta strand 3 and alpha helix 3, and a carboxyl-terminal Greek key beta-barrel domain.	Domain
A, B, C, D	PF16028	Solute carrier family 3 member 2 N-terminus (SLC3A2_N)	Solute carrier family 3 member 2 N-terminus	-	Family
F [auth L], H [auth I], J, L [auth K]	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

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	4F2 cell-surface antigen heavy chain	monoatomic cation transmembrane transporter activity metal cation:monoatomic cation antiporter activity calcium:monoatomic cation antiporter activity sodium ion transmembrane transporter activity secondary active transmembrane transporter activity antiporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity calcium ion transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity calcium:sodium antiporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity monoatomic cation transmembrane transporter activity metal cation:monoatomic cation antiporter activity calcium:monoatomic cation antiporter activity sodium ion transmembrane transporter activity secondary active transmembrane transporter activity antiporter activity active monoatomic ion transmembrane transporter activity active transmembrane transporter activity calcium ion transmembrane transporter activity inorganic molecular entity transmembrane transporter activity inorganic cation transmembrane transporter activity calcium:sodium antiporter activity monoatomic ion transmembrane transporter activity transporter activity metal ion transmembrane transporter activity transmembrane transporter activity RNA binding double-stranded RNA binding binding organic cyclic compound binding nucleic acid binding protein binding exogenous protein binding alanine transmembrane transporter activity L-amino acid transmembrane transporter activity organic cation transmembrane transporter activity carboxylic acid transmembrane transporter activity amino acid transmembrane transporter activity L-alanine transmembrane transporter activity neutral L-amino acid transmembrane transporter activity organic acid transmembrane transporter activity organic anion transmembrane transporter activity aromatic amino acid transmembrane transporter activity cell adhesion molecule binding cadherin binding virus receptor activity protein heterodimerization activity protein dimerization activity neutral L-amino acid secondary active transmembrane transporter activity identical protein binding protein homodimerization activity L-leucine transmembrane transporter activity branched-chain amino acid transmembrane transporter activity	nitrogen compound transport organic anion transport carboxylic acid transport transport organic substance transport neutral amino acid transport establishment of localization amino acid transport organic acid transport localization branched-chain amino acid transport isoleucine transport thyroid hormone transport regulation of hormone levels nitrogen compound transport organic anion transport carboxylic acid transport transport organic substance transport neutral amino acid transport establishment of localization amino acid transport organic acid transport localization branched-chain amino acid transport isoleucine transport thyroid hormone transport regulation of hormone levels biological regulation hormone transport regulation of biological quality methionine transport organic cation transport sulfur amino acid transport sulfur compound transport valine transport biological process involved in interspecies interaction between organisms symbiont entry into host cell viral process symbiont entry into host viral life cycle biological process involved in interaction with host biological process involved in symbiotic interaction aromatic amino acid transport tryptophan transport proline transport tyrosine transport L-amino acid transport carbohydrate metabolic process organic substance metabolic process primary metabolic process metabolic process phenylalanine transport response to organic substance response to stimulus response to chemical response to dsRNA response to nitrogen compound response to exogenous dsRNA response to organic cyclic compound import into cell carboxylic acid transmembrane transport amino acid transmembrane transport organic acid transmembrane transport L-alanine transmembrane transport import across plasma membrane L-alanine import across plasma membrane alanine transport transmembrane transport L-alanine transport L-alpha-amino acid transmembrane transport cellular process amino acid import across plasma membrane L-leucine transport L-leucine import across plasma membrane monoatomic ion transport monoatomic cation transport calcium ion transport metal ion transport L-histidine transport basic amino acid transport histidine transport	membrane cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery basal part of cell plasma membrane membrane cellular anatomical entity extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell periphery basal part of cell plasma membrane basal plasma membrane plasma membrane region basolateral plasma membrane vacuolar membrane intracellular anatomical structure lytic vacuole vacuole intracellular membrane-bounded organelle intracellular organelle lytic vacuole membrane bounding membrane of organelle lysosomal membrane cytoplasm organelle membrane lysosome somatodendritic compartment cell body cell pole apical pole of neuron neuronal cell body pigment granule intracellular vesicle melanosome cytoplasmic vesicle apical part of cell apical plasma membrane cell surface anchoring junction cell junction nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen synapse amino acid transport complex protein-containing complex plasma membrane protein complex membrane protein complex
E [auth H], G [auth E], I [auth F], K [auth G]	S1-F4 VH	-	-	-
F [auth L], H [auth I], J, L [auth K]	IGL c2062_light_IGKV4-1_IGKJ5	-	-	extracellular region cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR042280	Amino acid transporter heavy chain SLC3A2	Family
A, B, C, D	IPR031984	Solute carrier family 3 member 2, N-terminal domain	Domain
A, B, C, D	IPR017853	Glycoside hydrolase superfamily	Homologous Superfamily
A, B, C, D	IPR006047	Glycosyl hydrolase, family 13, catalytic domain	Domain
A, B, C, D	IPR013780	Glycosyl hydrolase, all-beta	Homologous Superfamily
F [auth L], H [auth I], J, L [auth K]	IPR013783	Immunoglobulin-like fold	Homologous Superfamily
F [auth L], H [auth I], J, L [auth K]	IPR036179	Immunoglobulin-like domain superfamily	Homologous Superfamily
F [auth L], H [auth I], J, L [auth K]	IPR003599	Immunoglobulin subtype	Domain
F [auth L], H [auth I], J, L [auth K]	IPR013106	Immunoglobulin V-set domain	Domain
F [auth L], H [auth I], J, L [auth K]	IPR007110	Immunoglobulin-like domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P08195	breast cancer Lung Neoplasms polycystic ovary syndrome diabetes mellitus malignant ependymoma tuberculosis lung benign neoplasm

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 R01GM133198.