1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Lay, F.T.
Schirra, H.J.
Scanlon, M.J.
Anderson, M.A.
Craik, D.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
UK
J.MOL.BIOL.
JMOBAK
0070
0022-2836
325
175
188
10.1016/S0022-2836(02)01103-8
12473460
The Three-dimensional Solution Structure of NaD1, a New Floral Defensin from Nicotiana alata and its Application to a Homology Model of the Crop Defense Protein alfAFP
2003
10.2210/pdb1mr4/pdb
pdb_00001mr4
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
5315.377
Nicotiana alata plant defensin 1 (NaD1)
residues 1-47
1
nat
polymer
Flower-specific gamma-thionin
no
no
RECKTESNTFPGICITKPPCRKACISEKFTDGHCSKILRRCLCTKPC
RECKTESNTFPGICITKPPCRKACISEKFTDGHCSKILRRCLCTKPC
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
common tobacco
Nicotiana
sample
4097
Nicotiana tabacum
Flower buds
database_2
pdbx_nmr_software
pdbx_struct_assembly
pdbx_struct_oper_list
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
1
0
2003-09-18
1
1
2008-04-28
1
2
2011-07-13
1
3
2022-02-23
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_nmr_software.name
_struct_ref_seq_dif.details
RCSB
Y
PDBJ
2002-09-18
REL
This structure was determined using standard 2D homonuclear techniques.
structures with the lowest energy
50
20
2D NOESY
DQF-COSY
2D NOESY
2D NOESY
2D NOESY
1mM
4
ambient
298
K
1mM
4
ambient
303
K
1mM
4
ambient
310
K
Simulated annealing with torsion angle dynamics and subsequent refinement in CNS
1mM NaD1, 90%H2O, 10%D2O
90% H2O/10% D2O
1mM NaD1, 99.9%D2O
99.9%D2O
Bruker
collection
XwinNMR
2.6
Bruker
processing
XwinNMR
2.6
Bartels
data analysis
XEASY
Brunger
structure solution
CNS
1.0
Brunger
refinement
CNS
1.0
Linge
data analysis
ARIA
500
Bruker
ARX
750
Bruker
DMX
ARG
1
n
1
ARG
1
A
GLU
2
n
2
GLU
2
A
CYS
3
n
3
CYS
3
A
LYS
4
n
4
LYS
4
A
THR
5
n
5
THR
5
A
GLU
6
n
6
GLU
6
A
SER
7
n
7
SER
7
A
ASN
8
n
8
ASN
8
A
THR
9
n
9
THR
9
A
PHE
10
n
10
PHE
10
A
PRO
11
n
11
PRO
11
A
GLY
12
n
12
GLY
12
A
ILE
13
n
13
ILE
13
A
CYS
14
n
14
CYS
14
A
ILE
15
n
15
ILE
15
A
THR
16
n
16
THR
16
A
LYS
17
n
17
LYS
17
A
PRO
18
n
18
PRO
18
A
PRO
19
n
19
PRO
19
A
CYS
20
n
20
CYS
20
A
ARG
21
n
21
ARG
21
A
LYS
22
n
22
LYS
22
A
ALA
23
n
23
ALA
23
A
CYS
24
n
24
CYS
24
A
ILE
25
n
25
ILE
25
A
SER
26
n
26
SER
26
A
GLU
27
n
27
GLU
27
A
LYS
28
n
28
LYS
28
A
PHE
29
n
29
PHE
29
A
THR
30
n
30
THR
30
A
ASP
31
n
31
ASP
31
A
GLY
32
n
32
GLY
32
A
HIS
33
n
33
HIS
33
A
CYS
34
n
34
CYS
34
A
SER
35
n
35
SER
35
A
LYS
36
n
36
LYS
36
A
ILE
37
n
37
ILE
37
A
LEU
38
n
38
LEU
38
A
ARG
39
n
39
ARG
39
A
ARG
40
n
40
ARG
40
A
CYS
41
n
41
CYS
41
A
LEU
42
n
42
LEU
42
A
CYS
43
n
43
CYS
43
A
THR
44
n
44
THR
44
A
LYS
45
n
45
LYS
45
A
PRO
46
n
46
PRO
46
A
CYS
47
n
47
CYS
47
A
author_defined_assembly
1
monomeric
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
N
THR
5
A
N
THR
5
A
O
CYS
43
A
O
CYS
43
A
O
LEU
42
A
O
LEU
42
A
N
HIS
33
A
N
HIS
33
2
A
A
H1
O
ARG
CYS
1
47
1.54
3
A
A
HZ2
HG
LYS
LEU
4
42
1.24
3
A
A
HE
OE1
ARG
GLU
1
2
1.55
3
A
A
OE1
HZ3
GLU
LYS
27
28
1.55
4
A
A
H1
OXT
ARG
CYS
1
47
1.50
4
A
A
OE2
HE
GLU
ARG
6
40
1.59
5
A
A
HE2
HG2
LYS
ARG
17
21
1.22
5
A
A
H1
OXT
ARG
CYS
1
47
1.53
5
A
A
OE1
HZ3
GLU
LYS
27
28
1.59
6
A
A
H2
OXT
ARG
CYS
1
47
1.52
7
A
A
H2
O
ARG
CYS
1
47
1.58
8
A
A
OE2
HZ1
GLU
LYS
2
4
1.55
9
A
A
H2
O
ARG
CYS
1
47
1.54
9
A
A
OE1
HZ1
GLU
LYS
2
4
1.57
10
A
A
H1
O
ARG
CYS
1
47
1.53
10
A
A
HE
OD1
ARG
ASP
21
31
1.59
10
A
A
OE1
HZ1
GLU
LYS
27
28
1.59
11
A
A
H2
O
ARG
CYS
1
47
1.53
11
A
A
HZ3
OD1
LYS
ASP
17
31
1.55
12
A
A
HZ2
O
LYS
GLY
17
32
1.59
12
A
A
OE2
HH21
GLU
ARG
6
40
1.60
13
A
A
OE1
HZ1
GLU
LYS
27
45
1.53
13
A
A
OE2
HZ2
GLU
LYS
27
28
1.58
14
A
A
HH12
OD1
ARG
ASP
21
31
1.59
15
A
A
OE1
HZ3
GLU
LYS
27
45
1.58
15
A
A
OE2
HZ3
GLU
LYS
27
28
1.60
16
A
A
H1
OXT
ARG
CYS
1
47
1.57
17
A
A
H3
OXT
ARG
CYS
1
47
1.54
17
A
A
HZ1
OE2
LYS
GLU
4
6
1.54
17
A
A
OE1
HZ2
GLU
LYS
27
28
1.55
20
A
A
H1
O
ARG
CYS
1
47
1.54
20
A
A
OE2
HZ2
GLU
LYS
27
28
1.60
1
A
PRO
11
-88.35
48.70
1
A
PHE
29
-138.91
-144.80
1
A
THR
30
-161.46
-48.57
1
A
LYS
36
-76.46
47.22
1
A
ILE
37
-135.28
-44.16
1
A
LEU
38
-135.09
-125.83
1
A
ARG
39
-150.99
52.21
2
A
PRO
11
-63.40
51.81
2
A
GLU
27
-80.57
-114.51
2
A
LYS
28
-143.30
46.47
2
A
PHE
29
-118.50
-141.55
2
A
THR
30
-159.05
-45.75
2
A
LYS
36
-84.08
33.07
2
A
ILE
37
-149.34
-46.13
2
A
PRO
46
-69.47
64.61
3
A
GLU
2
68.49
61.47
3
A
GLU
27
-84.73
-134.59
3
A
LYS
36
-81.46
33.03
3
A
ILE
37
-158.95
-42.21
3
A
PRO
46
-38.82
138.74
4
A
GLU
2
158.71
35.52
4
A
GLU
27
-85.92
-153.29
4
A
LYS
28
-103.71
55.96
4
A
PHE
29
-129.04
-128.54
4
A
THR
30
-178.26
-33.38
4
A
LYS
36
-77.22
47.65
4
A
ILE
37
-133.95
-40.69
4
A
LEU
38
-135.96
-123.63
4
A
ARG
39
-151.21
48.96
5
A
ASN
8
-91.28
46.22
5
A
THR
9
-154.71
-34.67
5
A
PHE
29
-128.33
-136.30
5
A
THR
30
-169.53
-42.06
5
A
HIS
33
179.44
160.68
5
A
LYS
36
-83.92
44.66
5
A
ILE
37
-146.71
-46.05
5
A
PRO
46
-69.63
65.63
6
A
GLU
27
-89.51
-125.85
6
A
PHE
29
-122.48
-146.04
6
A
THR
30
-152.65
-44.33
6
A
LYS
36
-85.92
31.01
6
A
ILE
37
-142.96
-50.90
7
A
SER
7
-69.76
95.59
7
A
ILE
15
-138.11
-44.62
7
A
GLU
27
-85.27
-152.85
7
A
PHE
29
-88.51
-143.32
7
A
THR
30
-170.88
-33.31
7
A
ILE
37
-145.75
-49.43
7
A
PRO
46
-69.87
68.66
8
A
ILE
15
-138.16
-47.15
8
A
PHE
29
-122.04
-136.16
8
A
THR
30
-164.95
-35.53
8
A
LYS
36
-85.54
34.52
8
A
ILE
37
-146.59
-48.66
9
A
GLU
2
172.65
34.32
9
A
GLU
27
-85.63
-138.71
9
A
LYS
28
-117.30
62.60
9
A
PHE
29
-134.16
-128.09
9
A
THR
30
-178.13
-31.88
9
A
LYS
36
-91.57
38.02
9
A
ILE
37
-142.64
-45.67
9
A
CYS
41
-67.59
95.43
10
A
PRO
11
-66.69
52.40
10
A
GLU
27
-80.46
-135.68
10
A
PHE
29
-137.50
-133.78
10
A
THR
30
-165.70
-38.96
10
A
LYS
36
-79.20
21.29
10
A
ILE
37
-153.32
-46.93
11
A
PRO
11
-68.55
50.09
11
A
GLU
27
-86.33
-145.78
11
A
LYS
28
-106.83
61.38
11
A
PHE
29
-130.76
-135.28
11
A
THR
30
-168.53
-31.36
11
A
LYS
36
-69.13
4.89
11
A
LEU
38
-146.77
-118.52
11
A
ARG
39
-150.90
45.86
12
A
SER
7
-35.52
132.26
12
A
GLU
27
-77.78
-143.69
12
A
PHE
29
-119.28
-139.76
12
A
THR
30
-163.67
-32.72
12
A
ILE
37
-146.79
-47.05
13
A
GLU
27
-74.94
-83.40
13
A
LYS
28
178.63
40.75
13
A
HIS
33
-176.36
149.44
13
A
ILE
37
-138.07
-47.88
13
A
LEU
38
-104.24
-141.51
13
A
ARG
39
-151.97
53.65
14
A
GLU
2
70.56
54.69
14
A
PRO
11
-69.26
49.53
14
A
PHE
29
-134.50
-143.37
14
A
THR
30
-166.03
-41.74
14
A
LYS
36
-82.77
35.99
14
A
ILE
37
-148.87
-47.57
15
A
PRO
11
-92.70
55.24
15
A
ILE
15
-131.05
-40.57
15
A
GLU
27
-67.29
-77.48
15
A
LYS
28
179.10
34.69
15
A
PHE
29
-105.93
-139.27
15
A
THR
30
-166.87
-38.68
15
A
LYS
36
-79.60
40.30
15
A
ILE
37
-146.39
-42.96
16
A
GLU
2
72.09
49.79
16
A
GLU
27
-79.65
-149.68
16
A
LYS
28
-108.13
55.46
16
A
PHE
29
-115.76
-144.80
16
A
THR
30
-162.01
-34.40
16
A
LYS
36
-74.29
46.88
16
A
ILE
37
-152.64
11.02
16
A
LEU
38
-174.96
-137.53
16
A
ARG
39
-151.50
56.45
17
A
GLU
27
-82.37
-132.70
17
A
PHE
29
-141.25
-140.74
17
A
THR
30
-164.03
-37.75
17
A
LYS
36
-78.05
46.76
17
A
ILE
37
-144.37
-44.25
17
A
LEU
38
-124.38
-133.84
17
A
ARG
39
-150.82
65.68
18
A
SER
7
-35.96
127.87
18
A
PHE
10
-35.10
113.01
18
A
GLU
27
-67.24
-90.62
18
A
LYS
28
-169.65
43.48
18
A
PHE
29
-114.66
-139.10
18
A
THR
30
-160.98
-31.13
18
A
LYS
36
-86.71
30.38
18
A
ILE
37
-140.68
-54.22
18
A
LEU
38
-95.71
-148.44
18
A
ARG
39
-151.49
55.83
19
A
PRO
11
-62.22
56.97
19
A
GLU
27
-83.91
-149.52
19
A
PHE
29
-95.27
-139.95
19
A
THR
30
-179.84
-41.39
19
A
HIS
33
-171.43
149.83
19
A
LYS
36
-90.14
30.49
19
A
ILE
37
-149.16
-51.15
20
A
ASN
8
-90.05
41.41
20
A
THR
9
-155.47
-41.40
20
A
GLU
27
-86.32
-158.82
20
A
PHE
29
-138.49
-139.08
20
A
THR
30
-169.62
-32.88
20
A
SER
35
54.46
137.39
20
A
LYS
36
-92.05
41.64
20
A
ILE
37
-158.00
-48.78
20
A
LEU
38
-122.77
-119.95
20
A
ARG
39
-150.86
56.20
Solution Structure of NaD1 from Nicotiana alata
1
N
N
A
THR
16
A
THR
16
HELX_P
A
GLU
27
A
GLU
27
1
1
12
disulf
2.026
A
CYS
3
A
SG
CYS
3
1_555
A
CYS
47
A
SG
CYS
47
1_555
disulf
2.032
A
CYS
14
A
SG
CYS
14
1_555
A
CYS
34
A
SG
CYS
34
1_555
disulf
2.029
A
CYS
20
A
SG
CYS
20
1_555
A
CYS
41
A
SG
CYS
41
1_555
disulf
2.027
A
CYS
24
A
SG
CYS
24
1_555
A
CYS
43
A
SG
CYS
43
1_555
PLANT PROTEIN
cysteine-stabilized alpha-beta motif, plant defensin fold, PLANT PROTEIN
THGF_TOBAC
UNP
1
26
P32026
RECKTESNTFPGICITKPPCRKACISEKFTDGHCSKLLRRCLCTKPC
26
72
1MR4
1
47
P32026
A
1
1
47
1
LEU
conflict
ILE
37
1MR4
A
P32026
UNP
62
37
3
anti-parallel
anti-parallel
A
CYS
3
A
CYS
3
A
GLU
6
A
GLU
6
A
CYS
41
A
CYS
41
A
LYS
45
A
LYS
45
A
ASP
31
A
ASP
31
A
CYS
34
A
CYS
34