5VYP | pdb_00005vyp

Crystal structure of the Plant Defensin NsD7 bound to PIP2

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
X	d5vypx1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
X	d5vypx2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
W	d5vypw1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
W	d5vypw2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
V	d5vypv1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
V	d5vypv2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
U	d5vypu1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
U	d5vypu2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
T	d5vypt1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
T	d5vypt2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
S	d5vyps1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
S	d5vyps2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
R	d5vypr1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
R	d5vypr2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
Q	d5vypq1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
Q	d5vypq2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
P	d5vypp1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
P	d5vypp2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
O	d5vypo1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
O	d5vypo2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
N	d5vypn_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
M	d5vypm_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
L	d5vypl_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
K	d5vypk1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
K	d5vypk2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
J	d5vypj1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
J	d5vypj2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
I	d5vypi1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
I	d5vypi2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
H	d5vyph1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
H	d5vyph2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
G	d5vypg1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
G	d5vypg2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
F	d5vypf1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
F	d5vypf2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
E	d5vype1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
E	d5vype2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
D	d5vypd1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
D	d5vypd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
C	d5vypc1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
C	d5vypc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
B	d5vypb1	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
B	d5vypb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)
A	d5vypa_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	Australian tobacco (Nicotiana suaveolens ) [TaxId: 200320 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
X	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
W	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
V	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
U	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
T	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	SCOP2B (2022-06-29)
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	SCOP2B Superfamily	Scorpion toxin-like	8078327	3000309	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)
X	Gamma-thionin	e5vypX1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
W	Gamma-thionin	e5vypW1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
V	Gamma-thionin	e5vypV1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
U	Gamma-thionin	e5vypU1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
T	Gamma-thionin	e5vypT1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
S	Gamma-thionin	e5vypS1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
R	Gamma-thionin	e5vypR1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
Q	Gamma-thionin	e5vypQ1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
P	Gamma-thionin	e5vypP1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
O	Gamma-thionin	e5vypO1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
N	Gamma-thionin	e5vypN1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
M	Gamma-thionin	e5vypM1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
L	Gamma-thionin	e5vypL1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
K	Gamma-thionin	e5vypK1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
J	Gamma-thionin	e5vypJ1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
I	Gamma-thionin	e5vypI1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
H	Gamma-thionin	e5vypH1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
G	Gamma-thionin	e5vypG1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
F	Gamma-thionin	e5vypF1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
E	Gamma-thionin	e5vypE1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
D	Gamma-thionin	e5vypD1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
C	Gamma-thionin	e5vypC1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
B	Gamma-thionin	e5vypB1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)
A	Gamma-thionin	e5vypA1	A: few secondary structure elements	X: omega toxin-like	H: omega toxin-related	T: Scorpion toxin-like	F: Gamma-thionin	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
X	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
W	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
V	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
U	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
T	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
S	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
R	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
Q	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
P	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
O	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
N	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
M	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
L	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
K	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
J	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
I	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
H	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
G	3.30.30.10	Alpha Beta	2-Layer Sandwich	Defensin A-like	Knottin, scorpion toxin-like	CATH (4.3.0)
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)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	PF00304	Gamma-thionin family (Gamma-thionin)	Gamma-thionin family		Domain

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, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	Defensin 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, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	IPR036574	Knottin, scorpion toxin-like superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	IPR003614	Knottins-like	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S, T, U, V, W, X	IPR008176	Defensin, plant	Family