3CCB

Crystal Structure of Human DPP4 in complex with a benzimidazole derivative

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3ccba1	All beta proteins	8-bladed beta-propeller	DPP6 N-terminal domain-like	DPP6 N-terminal domain-like	Dipeptidyl peptidase IV/CD26, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
A	d3ccba2	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	DPP6 catalytic domain-like	Dipeptidyl peptidase IV/CD26, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3ccbb1	All beta proteins	8-bladed beta-propeller	DPP6 N-terminal domain-like	DPP6 N-terminal domain-like	Dipeptidyl peptidase IV/CD26, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3ccbb2	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	DPP6 catalytic domain-like	Dipeptidyl peptidase IV/CD26, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
B	d3ccbb3	Artifacts	Tags	Tags	Tags	N-terminal Tags	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3ccbc1	All beta proteins	8-bladed beta-propeller	DPP6 N-terminal domain-like	DPP6 N-terminal domain-like	Dipeptidyl peptidase IV/CD26, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
C	d3ccbc2	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	DPP6 catalytic domain-like	Dipeptidyl peptidase IV/CD26, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3ccbd1	All beta proteins	8-bladed beta-propeller	DPP6 N-terminal domain-like	DPP6 N-terminal domain-like	Dipeptidyl peptidase IV/CD26, N-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)
D	d3ccbd2	Alpha and beta proteins (a/b)	alpha/beta-Hydrolases	alpha/beta-Hydrolases	DPP6 catalytic domain-like	Dipeptidyl peptidase IV/CD26, C-terminal domain	human (Homo sapiens ) [TaxId: 9606 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DPP6 N-terminal domain-like	8039749	3001705	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	alpha/beta-Hydrolases	8039750	3000102	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DPP6 N-terminal domain-like	8039749	3001705	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	alpha/beta-Hydrolases	8039750	3000102	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	DPP6 N-terminal domain-like	8039749	3001705	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	alpha/beta-Hydrolases	8039750	3000102	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	alpha/beta-Hydrolases	8039750	3000102	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	DPP6 N-terminal domain-like	8039749	3001705	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	DPPIV_N	e3ccbA1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: DPPIV_N	ECOD (1.6)
A	Hydrolase_4	e3ccbA2	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4	ECOD (1.6)
B	DPPIV_N	e3ccbB1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: DPPIV_N	ECOD (1.6)
B	Hydrolase_4	e3ccbB2	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4	ECOD (1.6)
C	DPPIV_N	e3ccbC1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: DPPIV_N	ECOD (1.6)
C	Hydrolase_4	e3ccbC2	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4	ECOD (1.6)
D	DPPIV_N	e3ccbD1	A: beta duplicates or obligate multimers	X: beta-propeller-like	H: beta-propeller	T: 8-bladed	F: DPPIV_N	ECOD (1.6)
D	Hydrolase_4	e3ccbD2	A: a/b three-layered sandwiches	X: alpha/beta-Hydrolases (From Topology)	H: alpha/beta-Hydrolases (From Topology)	T: alpha/beta-Hydrolases	F: Hydrolase_4	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	2.140.10.30	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
A	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)
B	2.140.10.30	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
B	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)
C	2.140.10.30	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
C	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)
D	2.140.10.30	Mainly Beta	8 Propeller	Methanol Dehydrogenase	Chain A	CATH (4.3.0)
D	3.40.50.1820	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	Alpha/Beta hydrolase fold, catalytic domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00930	Dipeptidyl peptidase IV (DPP IV) N-terminal region (DPPIV_N)	Dipeptidyl peptidase IV (DPP IV) N-terminal region	-	Repeat
A, B, C, D	PF00326	Prolyl oligopeptidase family (Peptidase_S9)	Prolyl oligopeptidase family	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Dipeptidyl peptidase 4	protein binding binding virus receptor activity exogenous protein binding peptidase activity catalytic activity, acting on a protein dipeptidyl-peptidase activity hydrolase activity exopeptidase activity catalytic activity signaling receptor binding enzyme binding protease binding serine hydrolase activity protein binding binding virus receptor activity exogenous protein binding peptidase activity catalytic activity, acting on a protein dipeptidyl-peptidase activity hydrolase activity exopeptidase activity catalytic activity signaling receptor binding enzyme binding protease binding serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity endopeptidase activity identical protein binding protein homodimerization activity protein dimerization activity molecular function activator activity molecular function regulator activity signaling receptor regulator activity chemorepellent activity receptor ligand activity signaling receptor activator activity aminopeptidase activity	membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization biological process involved in interaction with host vesicle-mediated transport biological process involved in symbiotic interaction membrane organization cellular component organization membrane fusion cellular process cellular component organization or biogenesis import into cell receptor-mediated endocytosis of virus by host cell biological process involved in interspecies interaction between organisms transport viral life cycle establishment of localization biological process involved in interaction with host vesicle-mediated transport biological process involved in symbiotic interaction localization symbiont entry into host cell viral process symbiont entry into host endocytosis involved in viral entry into host cell endocytosis receptor-mediated endocytosis transport of virus endothelial cell migration cell migration cell motility cellular response to stimulus negative regulation of locomotion regulation of cell motility regulation of cellular process response to stimulus negative regulation of biological process negative regulation of chemotaxis taxis regulation of immune system process negative regulation of cell migration chemotaxis regulation of biological process regulation of leukocyte chemotaxis regulation of leukocyte migration response to external stimulus neutrophil migration granulocyte migration leukocyte migration negative regulation of leukocyte migration regulation of response to stimulus regulation of locomotion response to chemical negative regulation of response to external stimulus regulation of neutrophil chemotaxis negative regulation of cell motility regulation of neutrophil migration negative regulation of neutrophil chemotaxis negative regulation of leukocyte chemotaxis regulation of response to external stimulus neutrophil chemotaxis regulation of granulocyte chemotaxis negative regulation of cellular process regulation of cell migration myeloid leukocyte migration locomotion cell chemotaxis negative regulation of response to stimulus negative regulation of granulocyte chemotaxis biological regulation regulation of chemotaxis cellular response to chemical stimulus negative regulation of immune system process immune system process granulocyte chemotaxis negative regulation of neutrophil migration leukocyte chemotaxis peptide hormone processing regulation of hormone levels signaling receptor ligand precursor processing primary metabolic process gene expression macromolecule biosynthetic process hormone metabolic process protein maturation biosynthetic process proteolysis protein processing metabolic process amide metabolic process protein metabolic process macromolecule metabolic process regulation of biological quality glucagon processing behavior multicellular organismal process locomotory behavior exploration behavior locomotory exploration behavior cell population proliferation positive regulation of cell population proliferation regulation of cell population proliferation positive regulation of biological process positive regulation of cellular process virion attachment to host cell receptor-mediated virion attachment to host cell adhesion of symbiont to host cell adhesion of symbiont to host T cell activation cell activation lymphocyte activation leukocyte activation cell adhesion response to decreased oxygen levels response to hypoxia response to stress response to oxygen levels response to abiotic stimulus psychomotor behavior motor behavior cell-cell adhesion mediated by integrin regulation of cell adhesion mediated by integrin regulation of cell adhesion regulation of cell-cell adhesion mediated by integrin cell-cell adhesion cell adhesion mediated by integrin regulation of cell-cell adhesion behavioral defense response fear response behavioral fear response defense response multicellular organismal response to stress cellular component disassembly negative regulation of extracellular matrix organization extracellular matrix disassembly regulation of cellular component organization negative regulation of cellular component organization extracellular matrix organization negative regulation of extracellular matrix disassembly regulation of extracellular matrix organization regulation of extracellular matrix disassembly extracellular structure organization external encapsulating structure organization regulation of leukocyte activation regulation of cell activation positive regulation of leukocyte cell-cell adhesion leukocyte cell-cell adhesion positive regulation of cell-cell adhesion positive regulation of lymphocyte activation positive regulation of cell activation positive regulation of leukocyte activation regulation of multicellular organismal process positive regulation of immune system process positive regulation of T cell activation positive regulation of cell adhesion regulation of T cell activation lymphocyte costimulation regulation of leukocyte cell-cell adhesion positive regulation of multicellular organismal process T cell costimulation regulation of lymphocyte activation	cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell-cell junction intercellular canaliculus cell projection cell leading edge plasma membrane bounded cell projection lamellipodium membrane cell periphery apical part of cell cellular anatomical structure anchoring junction cell junction focal adhesion cell-substrate junction cell-cell junction intercellular canaliculus cell projection cell leading edge plasma membrane bounded cell projection lamellipodium membrane cell periphery apical part of cell plasma membrane plasma membrane region apical plasma membrane extracellular exosome membrane-bounded organelle extracellular vesicle extracellular organelle extracellular region organelle extracellular space vesicle extracellular membrane-bounded organelle cell surface membrane microdomain membrane raft intracellular anatomical structure intracellular vesicle intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle cytoplasm endocytic vesicle leading edge membrane lamellipodium membrane cell projection membrane vacuolar membrane lytic vacuole vacuole lytic vacuole membrane bounding membrane of organelle lysosomal membrane organelle membrane lysosome

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001375	Peptidase S9, prolyl oligopeptidase, catalytic domain	Domain
A, B, C, D	IPR050278	Serine protease S9B/DPPIV	Family
A, B, C, D	IPR029058	Alpha/Beta hydrolase fold	Homologous Superfamily
A, B, C, D	IPR002471	Peptidase S9, serine active site	Active Site
A, B, C, D	IPR002469	Dipeptidylpeptidase IV, N-terminal domain	Domain

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B, C, D	Pharos: P27487	rheumatoid arthritis proteinuria type 2 diabetes mellitus malignant glioma Middle East respiratory syndrome ovarian cancer asthma common variable immunodeficiency cystic fibrosis glioblastoma hypoglycemia invasive ductal breast carcinoma lung cancer malignant mesothelioma non-small cell lung carcinoma rheumatoid arthritis proteinuria type 2 diabetes mellitus malignant glioma Middle East respiratory syndrome ovarian cancer asthma common variable immunodeficiency cystic fibrosis glioblastoma hypoglycemia invasive ductal breast carcinoma lung cancer malignant mesothelioma non-small cell lung carcinoma prediabetes syndrome tuberculosis Barrett esophagus coronary artery disease depressive disorder hyperglycemia inborn carbohydrate metabolic disorder kidney disease lung carcinoma Mental Depression obesity disorder cerebrovascular disorder COVID-19 hypertensive disorder interstitial cystitis lung adenocarcinoma

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.