4KKD | pdb_00004kkd

The X-ray crystal structure of Mannose-binding lectin-associated serine proteinase-3 reveals the structural basis for enzyme inactivity associated with the 3MC syndrome

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Pharos: Disease Associations

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
B	zf-C3HC4	e4kkdB1	A: a/b three-layered sandwiches	X: Thioredoxin-like	H: ClpP/crotonase	T: ClpP/crotonase	F: zf-C3HC4	ECOD (v294.1)
A	RCC1, RCC1_2, WD40_RLD	e4kkdA3	A: a/b three-layered sandwiches	X: PBZ domain	H: PBZ domain	T: PBZ domain	F: RCC1, RCC1_2, WD40_RLD	ECOD (v294.1)
A	V-set	e4kkdA6	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: V-set	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
B	2.10.70.10	Mainly Beta	Ribbon	Complement Module	domain 1	CATH (4.3.0)
B	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)
A	2.10.70.10	Mainly Beta	Ribbon	Complement Module	domain 1	CATH (4.3.0)
A	2.40.10.10	Mainly Beta	Beta Barrel	Thrombin, subunit H	Trypsin-like serine proteases	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF00084	Sushi repeat (SCR repeat) (Sushi)	Sushi repeat (SCR repeat)		Domain
A, B	PF00089	Trypsin (Trypsin)	Trypsin		Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Mannan-binding lectin serine protease 1	cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity endopeptidase activity cation binding ion binding binding calcium ion binding metal ion binding small molecule binding peptidase activity catalytic activity, acting on a protein hydrolase activity catalytic activity serine hydrolase activity serine-type peptidase activity serine-type endopeptidase activity endopeptidase activity identical protein binding protein binding protein homodimerization activity protein dimerization activity calcium-dependent protein binding	humoral immune response biological process involved in interspecies interaction between organisms response to stimulus positive regulation of biological process response to biotic stimulus positive regulation of response to stimulus complement activation positive regulation of immune response response to stress innate immune response regulation of immune system process response to external biotic stimulus positive regulation of immune system process complement activation, lectin pathway humoral immune response biological process involved in interspecies interaction between organisms response to stimulus positive regulation of biological process response to biotic stimulus positive regulation of response to stimulus complement activation positive regulation of immune response response to stress innate immune response regulation of immune system process response to external biotic stimulus positive regulation of immune system process complement activation, lectin pathway regulation of biological process immune response response to other organism defense response biological regulation defense response to symbiont response to external stimulus immune effector process regulation of response to stimulus immune system process defense response to other organism regulation of immune response activation of immune response regulation of humoral immune response regulation of immune effector process negative regulation of biological process negative regulation of complement activation negative regulation of response to stimulus negative regulation of immune response negative regulation of immune effector process negative regulation of humoral immune response negative regulation of immune system process regulation of complement activation biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process gene expression macromolecule biosynthetic process protein maturation complement activation, alternative pathway zymogen activation proteolysis protein processing	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol other organism part symbiont cell surface membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen cellular anatomical structure intracellular anatomical structure cytoplasm cytosol other organism part symbiont cell surface membrane-bounded organelle nucleus membrane-enclosed lumen intracellular membrane-bounded organelle intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen extracellular region extracellular space

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR018097	EGF-like calcium-binding, conserved site	Conserved Site
A, B	IPR035914	Spermadhesin, CUB domain superfamily	Homologous Superfamily
A, B	IPR000436	Sushi/SCR/CCP domain	Domain
A, B	IPR000859	CUB domain	Domain
A, B	IPR000742	EGF-like domain	Domain
A, B	IPR018114	Serine proteases, trypsin family, histidine active site	Active Site
A, B	IPR043504	Peptidase_S1_PA_chymotrypsin	Unknown
A, B	IPR035976	Sushi/SCR/CCP superfamily	Homologous Superfamily
A, B	IPR009003	Peptidase S1, PA clan	Homologous Superfamily
A, B	IPR001314	Peptidase S1A, chymotrypsin family	Family
A, B	IPR033116	Serine proteases, trypsin family, serine active site	Active Site
A, B	IPR001254	Serine proteases, trypsin domain	Domain
A, B	IPR001881	EGF-like calcium-binding domain	Domain
A, B	IPR024175	Peptidase S1A, complement C1r/C1S/mannan-binding	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P48740	3MC syndrome 3MC syndrome 1 3MC syndrome 3 Craniofacial Abnormalities oligodendroglioma astrocytic tumor glioblastoma malignant ependymoma nevus of Ito pancreatic ductal adenocarcinoma ulcerative colitis adrenoleukodystrophy breast cancer intellectual disability malignant glioma 3MC syndrome 3MC syndrome 1 3MC syndrome 3 Craniofacial Abnormalities oligodendroglioma astrocytic tumor glioblastoma malignant ependymoma nevus of Ito pancreatic ductal adenocarcinoma ulcerative colitis adrenoleukodystrophy breast cancer intellectual disability malignant glioma 3MC syndrome 2 amyotrophic lateral sclerosis breast fibroadenoma Ito hypomelanosis medulloblastoma

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.