1XX5

Crystal Structure of Natrin from Naja atra snake venom

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Membrane Protein Annotation: OPM

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d1xx5a1	Alpha and beta proteins (a+b)	PR-1-like	PR-1-like	PR-1-like	automated matches	(Naja atra ) [TaxId: 8656 ],	SCOPe (2.08)
A	d1xx5a2	Small proteins	Crisp domain-like	Crisp domain-like	automated matches	automated matches	(Naja atra ) [TaxId: 8656 ],	SCOPe (2.08)
B	d1xx5b1	Alpha and beta proteins (a+b)	PR-1-like	PR-1-like	PR-1-like	automated matches	(Naja atra ) [TaxId: 8656 ],	SCOPe (2.08)
B	d1xx5b2	Small proteins	Crisp domain-like	Crisp domain-like	automated matches	automated matches	(Naja atra ) [TaxId: 8656 ],	SCOPe (2.08)
C	d1xx5c1	Alpha and beta proteins (a+b)	PR-1-like	PR-1-like	PR-1-like	automated matches	(Naja atra ) [TaxId: 8656 ],	SCOPe (2.08)
C	d1xx5c2	Small proteins	Crisp domain-like	Crisp domain-like	automated matches	automated matches	(Naja atra ) [TaxId: 8656 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	CAP_1	e1xx5A1	A: a+b three layers	X: PR-1-like (From Topology)	H: PR-1-like (From Topology)	T: PR-1-like	F: CAP_1	ECOD (1.6)
A	Crisp	e1xx5A2	A: few secondary structure elements	X: Sea anemone toxin k-like	H: Sea anemone toxin k-related (From Topology)	T: Sea anemone toxin k-related	F: Crisp	ECOD (1.6)
B	CAP_1	e1xx5B1	A: a+b three layers	X: PR-1-like (From Topology)	H: PR-1-like (From Topology)	T: PR-1-like	F: CAP_1	ECOD (1.6)
B	Crisp	e1xx5B2	A: few secondary structure elements	X: Sea anemone toxin k-like	H: Sea anemone toxin k-related (From Topology)	T: Sea anemone toxin k-related	F: Crisp	ECOD (1.6)
C	CAP_1	e1xx5C1	A: a+b three layers	X: PR-1-like (From Topology)	H: PR-1-like (From Topology)	T: PR-1-like	F: CAP_1	ECOD (1.6)
C	Crisp	e1xx5C2	A: few secondary structure elements	X: Sea anemone toxin k-like	H: Sea anemone toxin k-related (From Topology)	T: Sea anemone toxin k-related	F: Crisp	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.33.10	Alpha Beta	3-Layer(aba) Sandwich	Pathogenesis-related Protein p14a	CAP	CATH (4.3.0)
A	1.10.10.740	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Crisp domain	CATH (4.3.0)
B	3.40.33.10	Alpha Beta	3-Layer(aba) Sandwich	Pathogenesis-related Protein p14a	CAP	CATH (4.3.0)
B	1.10.10.740	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Crisp domain	CATH (4.3.0)
C	3.40.33.10	Alpha Beta	3-Layer(aba) Sandwich	Pathogenesis-related Protein p14a	CAP	CATH (4.3.0)
C	1.10.10.740	Mainly Alpha	Orthogonal Bundle	Arc Repressor Mutant, subunit A	Crisp domain	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C	PF08562	Crisp (Crisp)	Crisp	This domain is found on Crisp proteins which contain Pfam:PF00188 and has been termed the Crisp domain. It is found in the mammalian reproductive tract and the venom of reptiles, and has been shown to regulate ryanodine receptor Ca2+ signalling [1]. ...	This domain is found on Crisp proteins which contain Pfam:PF00188 and has been termed the Crisp domain. It is found in the mammalian reproductive tract and the venom of reptiles, and has been shown to regulate ryanodine receptor Ca2+ signalling [1]. It contains 10 conserved cysteines which are all involved in disulphide bonds and is structurally related to the ion channel inhibitor toxins BgK and ShK [1].	Domain
A, B, C	PF00188	Cysteine-rich secretory protein family (CAP)	Cysteine-rich secretory protein family	This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organisms, including prokaryotes [2] and non-vertebrate eukaryotes [3], The nine subfamilies of the mam ...	This is a large family of cysteine-rich secretory proteins, antigen 5, and pathogenesis-related 1 proteins (CAP) that are found in a wide range of organisms, including prokaryotes [2] and non-vertebrate eukaryotes [3], The nine subfamilies of the mammalian CAP 'super'family include: the human glioma pathogenesis-related 1 (GLIPR1), Golgi associated pathogenesis related-1 (GAPR1) proteins, peptidase inhibitor 15 (PI15), peptidase inhibitor 16 (PI16), cysteine-rich secretory proteins (CRISPs), CRISP LCCL domain containing 1 (CRISPLD1), CRISP LCCL domain containing 2 (CRISPLD2), mannose receptor like and the R3H domain containing like proteins. Members are most often secreted and have an extracellular endocrine or paracrine function and are involved in processes including the regulation of extracellular matrix and branching morphogenesis, potentially as either proteases or protease inhibitors; in ion channel regulation in fertility; as tumour suppressor or pro-oncogenic genes in tissues including the prostate; and in cell-cell adhesion during fertilisation. The overall protein structural conservation within the CAP 'super'family results in fundamentally similar functions for the CAP domain in all members, yet the diversity outside of this core region dramatically alters the target specificity and, thus, the biological consequences [4]. The Ca++-chelating function [3] would fit with the various signalling processes (e.g. the CRISP proteins) that members of this family are involved in, and also the sequence and structural evidence of a conserved pocket containing two histidines and a glutamate. It also may explain how Swiss:Q91055 blocks the Ca++ transporting ryanodine receptors.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C	Natrin 1	potassium channel regulator activity channel regulator activity ion channel regulator activity molecular function regulator activity transporter regulator activity calcium channel regulator activity toxin activity	-	cellular anatomical structure extracellular region

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C	IPR013871	Cysteine-rich secretory protein	Domain
A, B, C	IPR003582	ShKT domain	Domain
A, B, C	IPR014044	CAP domain	Domain
A, B, C	IPR035940	CAP superfamily	Homologous Superfamily
A, B, C	IPR042076	Crisp-like domain	Homologous Superfamily
A, B, C	IPR034117	Cysteine-rich secretory protein, SCP domain	Domain
A, B, C	IPR001283	Cysteine-rich secretory protein-related	Family
A, B, C	IPR018244	Allergen V5/Tpx-1-related, conserved site	Conserved Site

Membrane Protein Annotation: OPM OPM Database Homepage

Chains	External Link	Type	Class	Superfamily	Family
A, B, C	OPM	Monotopic/peripheral	All alpha monotopic/peripheral	Sea anemone toxin-like proteins	Cysteine-rich secretory protein family

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.