5KK4 | pdb_00005kk4

Crystal Structure of the Plant Defensin NsD7 bound to Phosphatidic Acid

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
F	d5kk4f1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana suaveolens x Nicotiana tabacum ) [TaxId: 157071 ],	SCOPe (2.08)
F	d5kk4f2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Nicotiana suaveolens x Nicotiana tabacum ) [TaxId: 157071 ],	SCOPe (2.08)
E	d5kk4e1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana suaveolens x Nicotiana tabacum ) [TaxId: 157071 ],	SCOPe (2.08)
E	d5kk4e2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Nicotiana suaveolens x Nicotiana tabacum ) [TaxId: 157071 ],	SCOPe (2.08)
D	d5kk4d_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana suaveolens x Nicotiana tabacum ) [TaxId: 157071 ],	SCOPe (2.08)
C	d5kk4c_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana suaveolens x Nicotiana tabacum ) [TaxId: 157071 ],	SCOPe (2.08)
B	d5kk4b_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana suaveolens x Nicotiana tabacum ) [TaxId: 157071 ],	SCOPe (2.08)
A	d5kk4a_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana suaveolens x Nicotiana tabacum ) [TaxId: 157071 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
F	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
A	SCOP2 Family	Plant defensins	8078326	4003181	SCOP2 (2022-06-29)
A	SCOP2 Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2 (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
F	Ribosomal_L5,Ribosomal_L5_C	e5kk4F1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ribosomal_L5,Ribosomal_L5_C	ECOD (v294.1)
E	Ribosomal_L5,Ribosomal_L5_C	e5kk4E1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ribosomal_L5,Ribosomal_L5_C	ECOD (v294.1)
D	Ribosomal_L5,Ribosomal_L5_C	e5kk4D1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ribosomal_L5,Ribosomal_L5_C	ECOD (v294.1)
C	Ribosomal_L5,Ribosomal_L5_C	e5kk4C1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ribosomal_L5,Ribosomal_L5_C	ECOD (v294.1)
B	Ribosomal_L5,Ribosomal_L5_C	e5kk4B1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ribosomal_L5,Ribosomal_L5_C	ECOD (v294.1)
A	Ribosomal_L5,Ribosomal_L5_C	e5kk4A1	A: a/b three-layered sandwiches	X: cradle loop barrel	H: RIFT-related	T: Alanine racemase-C	F: Ribosomal_L5,Ribosomal_L5_C	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
F	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
E	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
D	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
C	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
B	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
A	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F	NsD7	ion binding binding anion binding phosphatidic acid binding phospholipid binding lipid binding small molecule binding	response to stimulus defense response response to stress biological process involved in interspecies interaction between organisms cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing	membrane-bounded organelle intracellular organelle cellular anatomical structure intracellular anatomical structure organelle vacuole cytoplasm intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F	IPR036574	Knottin, scorpion toxin-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F	IPR003614	Knottins-like	Domain
A, B, C, D, E A, B, C, D, E, F	IPR008176	Defensin, plant	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.