Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

5VYP

Crystal structure of the Plant Defensin NsD7 bound to PIP2

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0005773	cellular_component	vacuole
A	0006952	biological_process	defense response
A	0008289	molecular_function	lipid binding
A	0031640	biological_process	killing of cells of another organism
A	0070300	molecular_function	phosphatidic acid binding
B	0005773	cellular_component	vacuole
B	0006952	biological_process	defense response
B	0008289	molecular_function	lipid binding
B	0031640	biological_process	killing of cells of another organism
B	0070300	molecular_function	phosphatidic acid binding
C	0005773	cellular_component	vacuole
C	0006952	biological_process	defense response
C	0008289	molecular_function	lipid binding
C	0031640	biological_process	killing of cells of another organism
C	0070300	molecular_function	phosphatidic acid binding
D	0005773	cellular_component	vacuole
D	0006952	biological_process	defense response
D	0008289	molecular_function	lipid binding
D	0031640	biological_process	killing of cells of another organism
D	0070300	molecular_function	phosphatidic acid binding
E	0005773	cellular_component	vacuole
E	0006952	biological_process	defense response
E	0008289	molecular_function	lipid binding
E	0031640	biological_process	killing of cells of another organism
E	0070300	molecular_function	phosphatidic acid binding
F	0005773	cellular_component	vacuole
F	0006952	biological_process	defense response
F	0008289	molecular_function	lipid binding
F	0031640	biological_process	killing of cells of another organism
F	0070300	molecular_function	phosphatidic acid binding
G	0005773	cellular_component	vacuole
G	0006952	biological_process	defense response
G	0008289	molecular_function	lipid binding
G	0031640	biological_process	killing of cells of another organism
G	0070300	molecular_function	phosphatidic acid binding
H	0005773	cellular_component	vacuole
H	0006952	biological_process	defense response
H	0008289	molecular_function	lipid binding
H	0031640	biological_process	killing of cells of another organism
H	0070300	molecular_function	phosphatidic acid binding
I	0005773	cellular_component	vacuole
I	0006952	biological_process	defense response
I	0008289	molecular_function	lipid binding
I	0031640	biological_process	killing of cells of another organism
I	0070300	molecular_function	phosphatidic acid binding
J	0005773	cellular_component	vacuole
J	0006952	biological_process	defense response
J	0008289	molecular_function	lipid binding
J	0031640	biological_process	killing of cells of another organism
J	0070300	molecular_function	phosphatidic acid binding
K	0005773	cellular_component	vacuole
K	0006952	biological_process	defense response
K	0008289	molecular_function	lipid binding
K	0031640	biological_process	killing of cells of another organism
K	0070300	molecular_function	phosphatidic acid binding
L	0005773	cellular_component	vacuole
L	0006952	biological_process	defense response
L	0008289	molecular_function	lipid binding
L	0031640	biological_process	killing of cells of another organism
L	0070300	molecular_function	phosphatidic acid binding
M	0005773	cellular_component	vacuole
M	0006952	biological_process	defense response
M	0008289	molecular_function	lipid binding
M	0031640	biological_process	killing of cells of another organism
M	0070300	molecular_function	phosphatidic acid binding
N	0005773	cellular_component	vacuole
N	0006952	biological_process	defense response
N	0008289	molecular_function	lipid binding
N	0031640	biological_process	killing of cells of another organism
N	0070300	molecular_function	phosphatidic acid binding
O	0005773	cellular_component	vacuole
O	0006952	biological_process	defense response
O	0008289	molecular_function	lipid binding
O	0031640	biological_process	killing of cells of another organism
O	0070300	molecular_function	phosphatidic acid binding
P	0005773	cellular_component	vacuole
P	0006952	biological_process	defense response
P	0008289	molecular_function	lipid binding
P	0031640	biological_process	killing of cells of another organism
P	0070300	molecular_function	phosphatidic acid binding
Q	0005773	cellular_component	vacuole
Q	0006952	biological_process	defense response
Q	0008289	molecular_function	lipid binding
Q	0031640	biological_process	killing of cells of another organism
Q	0070300	molecular_function	phosphatidic acid binding
R	0005773	cellular_component	vacuole
R	0006952	biological_process	defense response
R	0008289	molecular_function	lipid binding
R	0031640	biological_process	killing of cells of another organism
R	0070300	molecular_function	phosphatidic acid binding
S	0005773	cellular_component	vacuole
S	0006952	biological_process	defense response
S	0008289	molecular_function	lipid binding
S	0031640	biological_process	killing of cells of another organism
S	0070300	molecular_function	phosphatidic acid binding
T	0005773	cellular_component	vacuole
T	0006952	biological_process	defense response
T	0008289	molecular_function	lipid binding
T	0031640	biological_process	killing of cells of another organism
T	0070300	molecular_function	phosphatidic acid binding
U	0005773	cellular_component	vacuole
U	0006952	biological_process	defense response
U	0008289	molecular_function	lipid binding
U	0031640	biological_process	killing of cells of another organism
U	0070300	molecular_function	phosphatidic acid binding
V	0005773	cellular_component	vacuole
V	0006952	biological_process	defense response
V	0008289	molecular_function	lipid binding
V	0031640	biological_process	killing of cells of another organism
V	0070300	molecular_function	phosphatidic acid binding
W	0005773	cellular_component	vacuole
W	0006952	biological_process	defense response
W	0008289	molecular_function	lipid binding
W	0031640	biological_process	killing of cells of another organism
W	0070300	molecular_function	phosphatidic acid binding
X	0005773	cellular_component	vacuole
X	0006952	biological_process	defense response
X	0008289	molecular_function	lipid binding
X	0031640	biological_process	killing of cells of another organism
X	0070300	molecular_function	phosphatidic acid binding

Functional Information from PDB Data

site_id	AC1
Number of Residues	13
Details	binding site for residue PIO A 101

Chain	Residue
A	LYS4
C	LYS36
D	PIO101
T	ILE37
X	PIO101
A	HIS33
A	SER35
A	LYS36
A	ILE37
A	LEU38
A	ARG40
B	ARG40
B	PIO101

site_id	AC2
Number of Residues	2
Details	binding site for residue SO4 A 102

Chain	Residue
A	PRO18
A	LYS22

site_id	AC3
Number of Residues	2
Details	binding site for residue SO4 A 103

Chain	Residue
A	PRO19
A	HOH202

site_id	AC4
Number of Residues	17
Details	binding site for residue PIO B 101

Chain	Residue
A	ARG40
A	PIO101
A	HOH201
B	LYS1
B	LYS4
B	HIS33
B	SER35
B	LYS36
B	ILE37
B	LEU38
B	ARG40
B	HOH204
C	LYS1
C	LYS36
C	HOH204
T	LEU38
V	LEU38

site_id	AC5
Number of Residues	18
Details	binding site for residue PIO C 101

Chain	Residue
B	LYS1
B	LYS36
C	LYS4
C	HIS33
C	SER35
C	LYS36
C	ILE37
C	LEU38
C	ARG40
C	HOH201
C	HOH204
D	ILE37
D	ARG40
D	PIO101
E	LYS36
F	PIO101
U	PIO101
X	PIO101

site_id	AC6
Number of Residues	5
Details	binding site for residue GOL C 102

Chain	Residue
A	LEU38
A	ARG40
C	ILE15
C	CYS34
C	ARG39

site_id	AC7
Number of Residues	16
Details	binding site for residue PIO D 101

Chain	Residue
A	PIO101
C	ARG40
C	PIO101
D	LYS1
D	LYS4
D	HIS33
D	SER35
D	LYS36
D	ILE37
D	LEU38
D	ARG40
E	LYS1
E	LYS36
E	HOH201
T	PIO101
V	PIO101

site_id	AC8
Number of Residues	2
Details	binding site for residue SO4 D 102

Chain	Residue
D	LEU38
R	SO4102

site_id	AC9
Number of Residues	14
Details	binding site for residue PIO E 101

Chain	Residue
D	LYS1
D	LYS36
E	LYS1
E	LYS4
E	HIS33
E	SER35
E	LYS36
E	ILE37
E	LEU38
E	ARG40
E	HOH201
F	ARG40
F	PIO101
G	LYS36

site_id	AD1
Number of Residues	13
Details	binding site for residue PIO F 101

Chain	Residue
F	ARG40
F	LEU42
G	LYS36
C	PIO101
D	LYS36
E	ARG40
E	PIO101
F	LYS4
F	HIS33
F	SER35
F	LYS36
F	ILE37
F	LEU38

site_id	AD2
Number of Residues	14
Details	binding site for residue PIO G 101

Chain	Residue
F	LYS36
G	LYS4
G	HIS33
G	SER35
G	LYS36
G	ILE37
G	LEU38
G	ARG40
G	LEU42
G	HOH201
H	ILE37
H	ARG40
H	PIO101
U	GOL106

site_id	AD3
Number of Residues	2
Details	binding site for residue SO4 G 102

Chain	Residue
U	SO4102
W	GOL102

site_id	AD4
Number of Residues	15
Details	binding site for residue PIO H 101

Chain	Residue
F	LYS36
F	ILE37
G	ARG40
G	PIO101
H	LYS1
H	LYS4
H	HIS33
H	SER35
H	LYS36
H	ILE37
H	LEU38
H	ARG40
I	LYS1
I	LYS36
P	PIO101

site_id	AD5
Number of Residues	16
Details	binding site for residue PIO I 101

Chain	Residue
H	LYS1
H	LYS36
I	LYS1
I	LYS4
I	HIS33
I	SER35
I	LYS36
I	ILE37
I	LEU38
I	ARG40
J	ILE37
J	ARG40
J	PIO101
K	LYS36
K	ILE37
K	PIO101

site_id	AD6
Number of Residues	2
Details	binding site for residue GOL I 102

Chain	Residue
I	LEU38
S	GOL102

site_id	AD7
Number of Residues	18
Details	binding site for residue PIO J 101

Chain	Residue
H	LYS36
I	ILE37
I	ARG40
I	PIO101
J	LYS4
J	HIS33
J	SER35
J	LYS36
J	ILE37
J	LEU38
J	ARG40
J	LEU42
J	HOH201
K	LYS1
K	LYS36
M	PIO101
O	PIO101
P	PIO101

site_id	AD8
Number of Residues	9
Details	binding site for residue PIO L 101

Chain	Residue
K	ARG40
K	PIO101
L	LYS4
L	HIS33
L	ILE37
L	LEU38
L	ARG40
M	PIO101
Q	LYS36

site_id	AD9
Number of Residues	15
Details	binding site for residue PIO M 101

Chain	Residue
J	ILE37
J	PIO101
L	PIO101
M	LYS4
M	HIS33
M	SER35
M	LYS36
M	ILE37
M	LEU38
M	ARG40
N	ARG40
N	PIO101
O	LYS36
O	ILE37
P	PIO101

site_id	AE1
Number of Residues	3
Details	binding site for residue GOL M 102

Chain	Residue
M	CYS47
M	HOH201
N	LYS28

site_id	AE2
Number of Residues	3
Details	binding site for residue GOL M 103

Chain	Residue
M	PRO18
M	PRO19
M	LYS22

site_id	AE3
Number of Residues	14
Details	binding site for residue PIO N 101

Chain	Residue
H	ILE13
M	ARG40
M	PIO101
N	LYS1
N	LYS4
N	HIS33
N	SER35
N	LYS36
N	ILE37
N	LEU38
N	ARG40
N	HOH201
O	LYS1
O	LYS36

site_id	AE4
Number of Residues	15
Details	binding site for residue PIO O 101

Chain	Residue
J	PIO101
N	LYS1
N	LYS36
O	LYS1
O	LYS4
O	HIS33
O	SER35
O	LYS36
O	ILE37
O	LEU38
O	ARG40
P	ILE37
P	ARG40
P	PIO101
R	PIO101

site_id	AE5
Number of Residues	19
Details	binding site for residue PIO P 101

Chain	Residue
H	PIO101
J	PIO101
M	PIO101
N	LYS36
N	ILE37
O	ILE37
O	ARG40
O	PIO101
P	LYS1
P	LYS4
P	HIS33
P	SER35
P	LYS36
P	ILE37
P	LEU38
P	ARG40
P	LEU42
Q	LYS1
Q	LYS36

site_id	AE6
Number of Residues	15
Details	binding site for residue PIO Q 101

Chain	Residue
P	LYS1
P	LYS36
Q	LYS1
Q	LYS4
Q	HIS33
Q	SER35
Q	LYS36
Q	ILE37
Q	LEU38
Q	ARG40
Q	HOH201
Q	HOH203
R	ARG40
R	PIO101
S	LYS36

site_id	AE7
Number of Residues	13
Details	binding site for residue PIO R 101

Chain	Residue
O	PIO101
Q	ILE37
Q	ARG40
Q	PIO101
R	LYS4
R	HIS33
R	SER35
R	LYS36
R	ILE37
R	LEU38
R	ARG40
R	HOH201
S	LYS36

site_id	AE8
Number of Residues	3
Details	binding site for residue SO4 R 102

Chain	Residue
D	SO4102
R	ILE37
R	LEU38

site_id	AE9
Number of Residues	15
Details	binding site for residue PIO S 101

Chain	Residue
R	LYS36
R	HOH201
S	LYS4
S	HIS33
S	SER35
S	LYS36
S	ILE37
S	LEU38
S	ARG40
S	LEU42
T	ILE37
T	ARG40
T	PIO101
U	LYS36
V	PIO101

site_id	AF1
Number of Residues	3
Details	binding site for residue GOL S 102

Chain	Residue
I	GOL102
S	ILE13
U	ILE15

site_id	AF2
Number of Residues	17
Details	binding site for residue PIO T 101

Chain	Residue
D	PIO101
R	LYS36
R	ILE37
S	ARG40
S	PIO101
T	LYS1
T	LYS4
T	HIS33
T	SER35
T	LYS36
T	ILE37
T	LEU38
T	ARG40
T	HOH203
U	LYS1
U	LYS36
U	HOH204

site_id	AF3
Number of Residues	8
Details	binding site for residue GOL T 102

Chain	Residue
T	ILE15
T	THR16
T	LYS17
T	HOH207
V	PHE10
V	GLY12
V	ILE13
V	LEU38

site_id	AF4
Number of Residues	16
Details	binding site for residue PIO U 101

Chain	Residue
C	PIO101
T	LYS36
U	LYS1
U	LYS4
U	HIS33
U	SER35
U	LYS36
U	ILE37
U	LEU38
U	ARG40
U	HOH204
V	ILE37
V	ARG40
V	PIO101
W	ILE37
X	PIO101

site_id	AF5
Number of Residues	5
Details	binding site for residue SO4 U 102

Chain	Residue
G	SO4102
U	ILE37
U	LEU38
U	HOH202
U	HOH207

site_id	AF6
Number of Residues	2
Details	binding site for residue SO4 U 103

Chain	Residue
P	LYS22
U	HOH203

site_id	AF7
Number of Residues	3
Details	binding site for residue SO4 U 104

Chain	Residue
B	LYS22
B	ARG26
U	LYS22

site_id	AF8
Number of Residues	2
Details	binding site for residue GOL U 105

Chain	Residue
U	LYS22
U	HOH203

site_id	AF9
Number of Residues	3
Details	binding site for residue GOL U 106

Chain	Residue
G	PIO101
U	LYS36
U	ILE37

site_id	AG1
Number of Residues	16
Details	binding site for residue PIO V 101

Chain	Residue
D	PIO101
S	PIO101
T	LYS36
T	ILE37
U	ILE37
U	ARG40
U	PIO101
V	LYS4
V	HIS33
V	SER35
V	LYS36
V	ILE37
V	LEU38
V	ARG40
W	LYS36
W	PIO101

site_id	AG2
Number of Residues	4
Details	binding site for residue GOL W 103

Chain	Residue
E	ILE13
W	LEU38
W	ARG40
X	PIO101

site_id	AG3
Number of Residues	16
Details	binding site for residue PIO X 101

Chain	Residue
A	PIO101
C	PIO101
E	LYS36
E	ILE37
U	PIO101
V	LYS36
W	ARG40
W	PIO101
W	GOL103
X	LYS4
X	HIS33
X	SER35
X	LYS36
X	ILE37
X	LEU38
X	ARG40

site_id	AG4
Number of Residues	35
Details	binding site for residues PIO K 101 and GOL Q 102

Chain	Residue
I	PIO101
J	LYS36
K	LYS1
K	LYS4
K	HIS33
K	SER35
K	LYS36
K	ILE37
K	LEU38
K	ARG40
L	ILE37
L	ARG40
L	PIO101
O	ILE13
O	LEU38
O	ARG40
P	LYS1
P	LYS36
Q	LYS1
Q	LYS4
Q	ILE13
Q	ILE15
Q	HIS33
Q	SER35
Q	LYS36
Q	ILE37
Q	LEU38
Q	ARG39
Q	ARG40
Q	HOH201
Q	HOH203
R	ARG40
R	PIO101
S	ILE15
S	LYS36

site_id	AG5
Number of Residues	18
Details	binding site for residues PIO W 101 and GOL W 102

Chain	Residue
E	ILE13
G	ARG39
G	SO4102
V	LYS36
V	PIO101
W	LYS1
W	LYS4
W	HIS33
W	SER35
W	LYS36
W	ILE37
W	LEU38
W	ARG40
W	LEU42
W	HOH201
X	ILE37
X	ARG40
X	PIO101

Functional Information from PROSITE/UniProt

site_id	PS00940
Number of Residues	24
Details	GAMMA_THIONIN Gamma-thionins family signature. KdCkreSntFp.GiCitkppCrkaC

Chain	Residue	Details
A	LYS1-CYS24

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	96
Details	Binding site: {"evidences":[{"source":"PubMed","id":"27647905","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	48
Details	Site: {"description":"Required for formation of double helix","evidences":[{"source":"PubMed","id":"27647905","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)