6B55 | pdb_00006b55

Crystal structure of the Plant Defensin NaD1 complexed with 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)
T	d6b55t_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
S	d6b55s_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
R	d6b55r_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
Q	d6b55q_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
P	d6b55p_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
O	d6b55o_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
N	d6b55n_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
M	d6b55m_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
L	d6b55l_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
K	d6b55k_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
J	d6b55j_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
I	d6b55i_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
H	d6b55h_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
G	d6b55g_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
F	d6b55f_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
E	d6b55e_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
D	d6b55d_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
C	d6b55c_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
B	d6b55b_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)
A	d6b55a_	Small proteins	Knottins (small inhibitors, toxins, lectins)	Scorpion toxin-like	Plant defensins	automated matches	(Nicotiana alata ) [TaxId: 4087 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
T	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Scorpion toxin-like	8078335	3000309	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Scorpion toxin-like	8078335	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)
T	DEAD	e6b55T1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
S	DEAD	e6b55S1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
R	DEAD	e6b55R1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
Q	DEAD	e6b55Q1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
P	DEAD	e6b55P1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
O	DEAD	e6b55O1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
N	DEAD	e6b55N1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
M	DEAD	e6b55M1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
L	DEAD	e6b55L1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
K	DEAD	e6b55K1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
J	DEAD	e6b55J1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
I	DEAD	e6b55I1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
H	DEAD	e6b55H1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
G	DEAD	e6b55G1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
F	DEAD	e6b55F1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
E	DEAD	e6b55E1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
D	DEAD	e6b55D1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
C	DEAD	e6b55C1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
B	DEAD	e6b55B1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: DEAD	ECOD (develop294)
A	Yippee-Mis18	e6b55A1	A: alpha bundles	X: Phosphorylase/hydrolase-like	H: Peptidyl-tRNA hydrolase-like	T: Peptidyl-tRNA hydrolase-like	F: Yippee-Mis18	ECOD (develop294)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
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)

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	Flower-specific defensin	-	defense response to fungus biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to stress response to external stimulus response to fungus response to external biotic stimulus response to biotic stimulus cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism defense response to fungus biological process involved in interspecies interaction between organisms response to stimulus response to other organism defense response response to stress response to external stimulus response to fungus response to external biotic stimulus response to biotic stimulus cellular process disruption of cell in another organism disruption of anatomical structure in another organism killing of cells of another organism cell killing	cellular anatomical structure extracellular region membrane-bounded organelle intracellular organelle 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	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	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	IPR008176	Defensin, plant	Family

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.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 6B55 | pdb_00006b55

Crystal structure of the Plant Defensin NaD1 complexed with phosphatidic acid

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

6B55 | pdb_00006b55