4XHS | pdb_00004xhs

Crystal structure of human NLRP12 PYD domain and implication in homotypic interaction

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	DEATH domain	8088520	3000069	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	DEATH domain	8088520	3000069	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	PYRIN	e4xhsA3	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: PYRIN	ECOD (1.6)
A	SBP_bac_1_C	e4xhsA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
A	SBP_bac_1_N_1	e4xhsA2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_N_1	ECOD (1.6)
B	PYRIN	e4xhsB3	A: alpha arrays	X: DEATH domain	H: DEATH domain (From Topology)	T: DEATH domain	F: PYRIN	ECOD (1.6)
B	SBP_bac_1_C	e4xhsB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_C	ECOD (1.6)
B	SBP_bac_1_N_1	e4xhsB2	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II (From Topology)	H: Periplasmic binding protein-like II (From Topology)	T: Periplasmic binding protein-like II	F: SBP_bac_1_N_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (utative)
B	3.40.190.10	Alpha Beta	3-Layer(aba) Sandwich	D-Maltodextrin-Binding Protein	domain 2	CATH (utative)
B	1.10.533.10	Mainly Alpha	Orthogonal Bundle	Death Domain, Fas	Death Domain, Fas	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B	PF02758	PAAD/DAPIN/Pyrin domain (PYRIN)	PAAD/DAPIN/Pyrin domain	This domain is predicted to contain 6 alpha helices and to have the same fold as the Pfam:PF00531 domain. This similarity may mean that this is a protein-protein interaction domain.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B	Maltose-binding periplasmic protein,NACHT, LRR and PYD domains-containing protein 12	cysteine-type endopeptidase activator activity endopeptidase activator activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity endopeptidase regulator activity protein-macromolecule adaptor activity molecular adaptor activity binding adenyl ribonucleotide binding nucleotide binding cysteine-type endopeptidase activator activity endopeptidase activator activity enzyme regulator activity enzyme activator activity peptidase regulator activity molecular function activator activity molecular function regulator activity peptidase activator activity endopeptidase regulator activity protein-macromolecule adaptor activity molecular adaptor activity 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	cellular response to stimulus regulation of signaling regulation of biological process regulation of cellular process response to stimulus negative regulation of signaling signaling negative regulation of response to stimulus biological regulation negative regulation of biological process regulation of signal transduction negative regulation of signal transduction negative regulation of cell communication cell communication regulation of response to stimulus cellular response to stimulus regulation of signaling regulation of biological process regulation of cellular process response to stimulus negative regulation of signaling signaling negative regulation of response to stimulus biological regulation negative regulation of biological process regulation of signal transduction negative regulation of signal transduction negative regulation of cell communication cell communication regulation of response to stimulus negative regulation of cellular process regulation of cell communication cellular process signal transduction regulation of defense response regulation of response to external stimulus defense response positive regulation of biological process response to external stimulus regulation of inflammatory response positive regulation of response to stimulus positive regulation of response to external stimulus positive regulation of inflammatory response regulation of response to stress response to stress positive regulation of defense response inflammatory response interleukin-6 production multicellular organismal process regulation of interleukin-6 production regulation of cytokine production cytokine production regulation of multicellular organismal process negative regulation of macromolecule metabolic process regulation of biosynthetic process negative regulation of metabolic process negative regulation of cytokine production regulation of macromolecule metabolic process gene expression macromolecule biosynthetic process regulation of gene expression negative regulation of interleukin-6 production negative regulation of gene expression biosynthetic process negative regulation of biosynthetic process negative regulation of macromolecule biosynthetic process regulation of macromolecule biosynthetic process metabolic process macromolecule metabolic process negative regulation of multicellular organismal process regulation of metabolic process intracellular signal transduction intracellular signaling cassette MAPK cascade ERK1 and ERK2 cascade negative regulation of intracellular signal transduction negative regulation of canonical NF-kappaB signal transduction regulation of intracellular signal transduction canonical NF-kappaB signal transduction regulation of canonical NF-kappaB signal transduction dendritic cell migration leukocyte migration immune system process mononuclear cell migration cell migration cell motility negative regulation of inflammatory response negative regulation of response to external stimulus negative regulation of defense response regulation of MAPK cascade negative regulation of ERK1 and ERK2 cascade regulation of ERK1 and ERK2 cascade negative regulation of MAPK cascade interleukin-1 production regulation of interleukin-1 beta production positive regulation of macromolecule biosynthetic process positive regulation of metabolic process positive regulation of interleukin-1 beta production positive regulation of biosynthetic process positive regulation of interleukin-1 production positive regulation of macromolecule metabolic process positive regulation of cellular process regulation of interleukin-1 production interleukin-1 beta production positive regulation of gene expression positive regulation of multicellular organismal process positive regulation of cytokine production negative regulation of interleukin-1 production positive regulation of cell communication positive regulation of signal transduction regulation of non-canonical NF-kappaB signal transduction non-canonical NF-kappaB signal transduction positive regulation of intracellular signal transduction positive regulation of non-canonical NF-kappaB signal transduction positive regulation of signaling positive regulation of MHC class I biosynthetic process regulation of MHC class I biosynthetic process MHC class I biosynthetic process regulation of interleukin-18 production interleukin-18 production negative regulation of non-canonical NF-kappaB signal transduction negative regulation of Toll signaling pathway regulation of Toll signaling pathway cell surface receptor signaling pathway Toll signaling pathway response to peptide response to chemical response to cytokine cellular response to cytokine stimulus	cellular anatomical structure intracellular anatomical structure cytoplasm cytosol

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B	IPR004020	DAPIN domain	Domain
A, B	IPR029495	NACHT-associated domain	Domain
A, B	IPR007111	NACHT nucleoside triphosphatase	Domain
A, B	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B	IPR011029	Death-like domain superfamily	Homologous Superfamily
A, B	IPR041267	NACHT, LRR and PYD domains-containing protein, helical domain HD2	Domain
A, B	IPR001611	Leucine-rich repeat	Repeat
A, B	IPR041075	NOD1/2, winged helix domain	Domain
A, B	IPR032675	Leucine-rich repeat domain superfamily	Homologous Superfamily
A, B	IPR050637	NLRP family, innate immunity and inflammation regulators	Family

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, B	Pharos: P59046	familial cold autoinflammatory syndrome 2 renal cell carcinoma collecting duct carcinoma sarcomatoid renal cell carcinoma chromophobe renal cell carcinoma papillary renal cell carcinoma childhood-onset schizophrenia periodic fever syndrome osteosarcoma renal carcinoma testicular germ cell tumor clear cell renal carcinoma familial cold autoinflammatory syndrome tuberculosis

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.