Loading
PDBj
MenuPDBj@FacebookPDBj@TwitterPDBj@YouTubewwPDB FoundationwwPDB
RCSB PDBPDBeBMRBAdv. SearchSearch help

5VYP

Crystal structure of the Plant Defensin NsD7 bound to PIP2

Functional Information from GO Data
ChainGOidnamespacecontents
A0005773cellular_componentvacuole
A0006952biological_processdefense response
A0008289molecular_functionlipid binding
A0031640biological_processkilling of cells of another organism
A0070300molecular_functionphosphatidic acid binding
B0005773cellular_componentvacuole
B0006952biological_processdefense response
B0008289molecular_functionlipid binding
B0031640biological_processkilling of cells of another organism
B0070300molecular_functionphosphatidic acid binding
C0005773cellular_componentvacuole
C0006952biological_processdefense response
C0008289molecular_functionlipid binding
C0031640biological_processkilling of cells of another organism
C0070300molecular_functionphosphatidic acid binding
D0005773cellular_componentvacuole
D0006952biological_processdefense response
D0008289molecular_functionlipid binding
D0031640biological_processkilling of cells of another organism
D0070300molecular_functionphosphatidic acid binding
E0005773cellular_componentvacuole
E0006952biological_processdefense response
E0008289molecular_functionlipid binding
E0031640biological_processkilling of cells of another organism
E0070300molecular_functionphosphatidic acid binding
F0005773cellular_componentvacuole
F0006952biological_processdefense response
F0008289molecular_functionlipid binding
F0031640biological_processkilling of cells of another organism
F0070300molecular_functionphosphatidic acid binding
G0005773cellular_componentvacuole
G0006952biological_processdefense response
G0008289molecular_functionlipid binding
G0031640biological_processkilling of cells of another organism
G0070300molecular_functionphosphatidic acid binding
H0005773cellular_componentvacuole
H0006952biological_processdefense response
H0008289molecular_functionlipid binding
H0031640biological_processkilling of cells of another organism
H0070300molecular_functionphosphatidic acid binding
I0005773cellular_componentvacuole
I0006952biological_processdefense response
I0008289molecular_functionlipid binding
I0031640biological_processkilling of cells of another organism
I0070300molecular_functionphosphatidic acid binding
J0005773cellular_componentvacuole
J0006952biological_processdefense response
J0008289molecular_functionlipid binding
J0031640biological_processkilling of cells of another organism
J0070300molecular_functionphosphatidic acid binding
K0005773cellular_componentvacuole
K0006952biological_processdefense response
K0008289molecular_functionlipid binding
K0031640biological_processkilling of cells of another organism
K0070300molecular_functionphosphatidic acid binding
L0005773cellular_componentvacuole
L0006952biological_processdefense response
L0008289molecular_functionlipid binding
L0031640biological_processkilling of cells of another organism
L0070300molecular_functionphosphatidic acid binding
M0005773cellular_componentvacuole
M0006952biological_processdefense response
M0008289molecular_functionlipid binding
M0031640biological_processkilling of cells of another organism
M0070300molecular_functionphosphatidic acid binding
N0005773cellular_componentvacuole
N0006952biological_processdefense response
N0008289molecular_functionlipid binding
N0031640biological_processkilling of cells of another organism
N0070300molecular_functionphosphatidic acid binding
O0005773cellular_componentvacuole
O0006952biological_processdefense response
O0008289molecular_functionlipid binding
O0031640biological_processkilling of cells of another organism
O0070300molecular_functionphosphatidic acid binding
P0005773cellular_componentvacuole
P0006952biological_processdefense response
P0008289molecular_functionlipid binding
P0031640biological_processkilling of cells of another organism
P0070300molecular_functionphosphatidic acid binding
Q0005773cellular_componentvacuole
Q0006952biological_processdefense response
Q0008289molecular_functionlipid binding
Q0031640biological_processkilling of cells of another organism
Q0070300molecular_functionphosphatidic acid binding
R0005773cellular_componentvacuole
R0006952biological_processdefense response
R0008289molecular_functionlipid binding
R0031640biological_processkilling of cells of another organism
R0070300molecular_functionphosphatidic acid binding
S0005773cellular_componentvacuole
S0006952biological_processdefense response
S0008289molecular_functionlipid binding
S0031640biological_processkilling of cells of another organism
S0070300molecular_functionphosphatidic acid binding
T0005773cellular_componentvacuole
T0006952biological_processdefense response
T0008289molecular_functionlipid binding
T0031640biological_processkilling of cells of another organism
T0070300molecular_functionphosphatidic acid binding
U0005773cellular_componentvacuole
U0006952biological_processdefense response
U0008289molecular_functionlipid binding
U0031640biological_processkilling of cells of another organism
U0070300molecular_functionphosphatidic acid binding
V0005773cellular_componentvacuole
V0006952biological_processdefense response
V0008289molecular_functionlipid binding
V0031640biological_processkilling of cells of another organism
V0070300molecular_functionphosphatidic acid binding
W0005773cellular_componentvacuole
W0006952biological_processdefense response
W0008289molecular_functionlipid binding
W0031640biological_processkilling of cells of another organism
W0070300molecular_functionphosphatidic acid binding
X0005773cellular_componentvacuole
X0006952biological_processdefense response
X0008289molecular_functionlipid binding
X0031640biological_processkilling of cells of another organism
X0070300molecular_functionphosphatidic acid binding
Functional Information from PDB Data
site_idAC1
Number of Residues13
Detailsbinding site for residue PIO A 101
ChainResidue
ALYS4
CLYS36
DPIO101
TILE37
XPIO101
AHIS33
ASER35
ALYS36
AILE37
ALEU38
AARG40
BARG40
BPIO101

site_idAC2
Number of Residues2
Detailsbinding site for residue SO4 A 102
ChainResidue
APRO18
ALYS22

site_idAC3
Number of Residues2
Detailsbinding site for residue SO4 A 103
ChainResidue
APRO19
AHOH202

site_idAC4
Number of Residues17
Detailsbinding site for residue PIO B 101
ChainResidue
AARG40
APIO101
AHOH201
BLYS1
BLYS4
BHIS33
BSER35
BLYS36
BILE37
BLEU38
BARG40
BHOH204
CLYS1
CLYS36
CHOH204
TLEU38
VLEU38

site_idAC5
Number of Residues18
Detailsbinding site for residue PIO C 101
ChainResidue
BLYS1
BLYS36
CLYS4
CHIS33
CSER35
CLYS36
CILE37
CLEU38
CARG40
CHOH201
CHOH204
DILE37
DARG40
DPIO101
ELYS36
FPIO101
UPIO101
XPIO101

site_idAC6
Number of Residues5
Detailsbinding site for residue GOL C 102
ChainResidue
ALEU38
AARG40
CILE15
CCYS34
CARG39

site_idAC7
Number of Residues16
Detailsbinding site for residue PIO D 101
ChainResidue
APIO101
CARG40
CPIO101
DLYS1
DLYS4
DHIS33
DSER35
DLYS36
DILE37
DLEU38
DARG40
ELYS1
ELYS36
EHOH201
TPIO101
VPIO101

site_idAC8
Number of Residues2
Detailsbinding site for residue SO4 D 102
ChainResidue
DLEU38
RSO4102

site_idAC9
Number of Residues14
Detailsbinding site for residue PIO E 101
ChainResidue
DLYS1
DLYS36
ELYS1
ELYS4
EHIS33
ESER35
ELYS36
EILE37
ELEU38
EARG40
EHOH201
FARG40
FPIO101
GLYS36

site_idAD1
Number of Residues13
Detailsbinding site for residue PIO F 101
ChainResidue
FARG40
FLEU42
GLYS36
CPIO101
DLYS36
EARG40
EPIO101
FLYS4
FHIS33
FSER35
FLYS36
FILE37
FLEU38

site_idAD2
Number of Residues14
Detailsbinding site for residue PIO G 101
ChainResidue
FLYS36
GLYS4
GHIS33
GSER35
GLYS36
GILE37
GLEU38
GARG40
GLEU42
GHOH201
HILE37
HARG40
HPIO101
UGOL106

site_idAD3
Number of Residues2
Detailsbinding site for residue SO4 G 102
ChainResidue
USO4102
WGOL102

site_idAD4
Number of Residues15
Detailsbinding site for residue PIO H 101
ChainResidue
FLYS36
FILE37
GARG40
GPIO101
HLYS1
HLYS4
HHIS33
HSER35
HLYS36
HILE37
HLEU38
HARG40
ILYS1
ILYS36
PPIO101

site_idAD5
Number of Residues16
Detailsbinding site for residue PIO I 101
ChainResidue
HLYS1
HLYS36
ILYS1
ILYS4
IHIS33
ISER35
ILYS36
IILE37
ILEU38
IARG40
JILE37
JARG40
JPIO101
KLYS36
KILE37
KPIO101

site_idAD6
Number of Residues2
Detailsbinding site for residue GOL I 102
ChainResidue
ILEU38
SGOL102

site_idAD7
Number of Residues18
Detailsbinding site for residue PIO J 101
ChainResidue
HLYS36
IILE37
IARG40
IPIO101
JLYS4
JHIS33
JSER35
JLYS36
JILE37
JLEU38
JARG40
JLEU42
JHOH201
KLYS1
KLYS36
MPIO101
OPIO101
PPIO101

site_idAD8
Number of Residues9
Detailsbinding site for residue PIO L 101
ChainResidue
KARG40
KPIO101
LLYS4
LHIS33
LILE37
LLEU38
LARG40
MPIO101
QLYS36

site_idAD9
Number of Residues15
Detailsbinding site for residue PIO M 101
ChainResidue
JILE37
JPIO101
LPIO101
MLYS4
MHIS33
MSER35
MLYS36
MILE37
MLEU38
MARG40
NARG40
NPIO101
OLYS36
OILE37
PPIO101

site_idAE1
Number of Residues3
Detailsbinding site for residue GOL M 102
ChainResidue
MCYS47
MHOH201
NLYS28

site_idAE2
Number of Residues3
Detailsbinding site for residue GOL M 103
ChainResidue
MPRO18
MPRO19
MLYS22

site_idAE3
Number of Residues14
Detailsbinding site for residue PIO N 101
ChainResidue
HILE13
MARG40
MPIO101
NLYS1
NLYS4
NHIS33
NSER35
NLYS36
NILE37
NLEU38
NARG40
NHOH201
OLYS1
OLYS36

site_idAE4
Number of Residues15
Detailsbinding site for residue PIO O 101
ChainResidue
JPIO101
NLYS1
NLYS36
OLYS1
OLYS4
OHIS33
OSER35
OLYS36
OILE37
OLEU38
OARG40
PILE37
PARG40
PPIO101
RPIO101

site_idAE5
Number of Residues19
Detailsbinding site for residue PIO P 101
ChainResidue
HPIO101
JPIO101
MPIO101
NLYS36
NILE37
OILE37
OARG40
OPIO101
PLYS1
PLYS4
PHIS33
PSER35
PLYS36
PILE37
PLEU38
PARG40
PLEU42
QLYS1
QLYS36

site_idAE6
Number of Residues15
Detailsbinding site for residue PIO Q 101
ChainResidue
PLYS1
PLYS36
QLYS1
QLYS4
QHIS33
QSER35
QLYS36
QILE37
QLEU38
QARG40
QHOH201
QHOH203
RARG40
RPIO101
SLYS36

site_idAE7
Number of Residues13
Detailsbinding site for residue PIO R 101
ChainResidue
OPIO101
QILE37
QARG40
QPIO101
RLYS4
RHIS33
RSER35
RLYS36
RILE37
RLEU38
RARG40
RHOH201
SLYS36

site_idAE8
Number of Residues3
Detailsbinding site for residue SO4 R 102
ChainResidue
DSO4102
RILE37
RLEU38

site_idAE9
Number of Residues15
Detailsbinding site for residue PIO S 101
ChainResidue
RLYS36
RHOH201
SLYS4
SHIS33
SSER35
SLYS36
SILE37
SLEU38
SARG40
SLEU42
TILE37
TARG40
TPIO101
ULYS36
VPIO101

site_idAF1
Number of Residues3
Detailsbinding site for residue GOL S 102
ChainResidue
IGOL102
SILE13
UILE15

site_idAF2
Number of Residues17
Detailsbinding site for residue PIO T 101
ChainResidue
DPIO101
RLYS36
RILE37
SARG40
SPIO101
TLYS1
TLYS4
THIS33
TSER35
TLYS36
TILE37
TLEU38
TARG40
THOH203
ULYS1
ULYS36
UHOH204

site_idAF3
Number of Residues8
Detailsbinding site for residue GOL T 102
ChainResidue
TILE15
TTHR16
TLYS17
THOH207
VPHE10
VGLY12
VILE13
VLEU38

site_idAF4
Number of Residues16
Detailsbinding site for residue PIO U 101
ChainResidue
CPIO101
TLYS36
ULYS1
ULYS4
UHIS33
USER35
ULYS36
UILE37
ULEU38
UARG40
UHOH204
VILE37
VARG40
VPIO101
WILE37
XPIO101

site_idAF5
Number of Residues5
Detailsbinding site for residue SO4 U 102
ChainResidue
GSO4102
UILE37
ULEU38
UHOH202
UHOH207

site_idAF6
Number of Residues2
Detailsbinding site for residue SO4 U 103
ChainResidue
PLYS22
UHOH203

site_idAF7
Number of Residues3
Detailsbinding site for residue SO4 U 104
ChainResidue
BLYS22
BARG26
ULYS22

site_idAF8
Number of Residues2
Detailsbinding site for residue GOL U 105
ChainResidue
ULYS22
UHOH203

site_idAF9
Number of Residues3
Detailsbinding site for residue GOL U 106
ChainResidue
GPIO101
ULYS36
UILE37

site_idAG1
Number of Residues16
Detailsbinding site for residue PIO V 101
ChainResidue
DPIO101
SPIO101
TLYS36
TILE37
UILE37
UARG40
UPIO101
VLYS4
VHIS33
VSER35
VLYS36
VILE37
VLEU38
VARG40
WLYS36
WPIO101

site_idAG2
Number of Residues4
Detailsbinding site for residue GOL W 103
ChainResidue
EILE13
WLEU38
WARG40
XPIO101

site_idAG3
Number of Residues16
Detailsbinding site for residue PIO X 101
ChainResidue
APIO101
CPIO101
ELYS36
EILE37
UPIO101
VLYS36
WARG40
WPIO101
WGOL103
XLYS4
XHIS33
XSER35
XLYS36
XILE37
XLEU38
XARG40

site_idAG4
Number of Residues35
Detailsbinding site for residues PIO K 101 and GOL Q 102
ChainResidue
IPIO101
JLYS36
KLYS1
KLYS4
KHIS33
KSER35
KLYS36
KILE37
KLEU38
KARG40
LILE37
LARG40
LPIO101
OILE13
OLEU38
OARG40
PLYS1
PLYS36
QLYS1
QLYS4
QILE13
QILE15
QHIS33
QSER35
QLYS36
QILE37
QLEU38
QARG39
QARG40
QHOH201
QHOH203
RARG40
RPIO101
SILE15
SLYS36

site_idAG5
Number of Residues18
Detailsbinding site for residues PIO W 101 and GOL W 102
ChainResidue
EILE13
GARG39
GSO4102
VLYS36
VPIO101
WLYS1
WLYS4
WHIS33
WSER35
WLYS36
WILE37
WLEU38
WARG40
WLEU42
WHOH201
XILE37
XARG40
XPIO101

Functional Information from PROSITE/UniProt
site_idPS00940
Number of Residues24
DetailsGAMMA_THIONIN Gamma-thionins family signature. KdCkreSntFp.GiCitkppCrkaC
ChainResidueDetails
ALYS1-CYS24

Functional Information from SwissProt/UniProt
site_idSWS_FT_FI1
Number of Residues96
DetailsBINDING: BINDING => ECO:0000269|PubMed:27647905
ChainResidueDetails
ALYS4
CHIS33
CLYS36
CARG39
DLYS4
DHIS33
DLYS36
DARG39
ELYS4
EHIS33
ELYS36
AHIS33
EARG39
FLYS4
FHIS33
FLYS36
FARG39
GLYS4
GHIS33
GLYS36
GARG39
HLYS4
ALYS36
HHIS33
HLYS36
HARG39
ILYS4
IHIS33
ILYS36
IARG39
JLYS4
JHIS33
JLYS36
AARG39
JARG39
KLYS4
KHIS33
KLYS36
KARG39
LLYS4
LHIS33
LLYS36
LARG39
MLYS4
BLYS4
MHIS33
MLYS36
MARG39
NLYS4
NHIS33
NLYS36
NARG39
OLYS4
OHIS33
OLYS36
BHIS33
OARG39
PLYS4
PHIS33
PLYS36
PARG39
QLYS4
QHIS33
QLYS36
QARG39
RLYS4
BLYS36
RHIS33
RLYS36
RARG39
SLYS4
SHIS33
SLYS36
SARG39
TLYS4
THIS33
TLYS36
BARG39
TARG39
ULYS4
UHIS33
ULYS36
UARG39
VLYS4
VHIS33
VLYS36
VARG39
WLYS4
CLYS4
WHIS33
WLYS36
WARG39
XLYS4
XHIS33
XLYS36
XARG39

site_idSWS_FT_FI2
Number of Residues48
DetailsSITE: Required for formation of double helix => ECO:0000269|PubMed:27647905
ChainResidueDetails
AILE15
EILE37
FILE15
FILE37
GILE15
GILE37
HILE15
HILE37
IILE15
IILE37
JILE15
AILE37
JILE37
KILE15
KILE37
LILE15
LILE37
MILE15
MILE37
NILE15
NILE37
OILE15
BILE15
OILE37
PILE15
PILE37
QILE15
QILE37
RILE15
RILE37
SILE15
SILE37
TILE15
BILE37
TILE37
UILE15
UILE37
VILE15
VILE37
WILE15
WILE37
XILE15
XILE37
CILE15
CILE37
DILE15
DILE37
EILE15

217705

PDB entries from 2024-03-27

PDB statisticsPDBj update infoContact PDBjnumon