1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Kohda, D.
Fujinami, D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
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
C3 H7 N O2
89.093
D-ALANINE
D-peptide linking
C4 H9 N O2
103.120
D-ALPHA-AMINOBUTYRIC ACID
D-peptide linking
C4 H7 N O2
101.104
n
(2Z)-2-AMINOBUT-2-ENOIC ACID
Z-DEHYDROBUTYRINE
peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
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 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
Commun Biol
2399-3642
1
150
150
10.1038/s42003-018-0150-3
30272026
The lantibiotic nukacin ISK-1 exists in an equilibrium between active and inactive lipid-II binding states.
2018
0000-0002-6763-2577
0000-0001-8234-3776
10.2210/pdb5z5q/pdb
pdb_00005z5q
2970.535
Lantibiotic nukacin
1
nat
polymer
Bacteriocin ISK-1
no
yes
KKKSGVIP(DBB)V(DAL)HDCHMN(DAL)FQFVF(DBU)CCS
KKKSGVIPTVAHDCHMNAFQFVFTCCS
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
sample
1
27
1292
Staphylococcus warneri
database_2
pdbx_database_status
pdbx_nmr_spectrometer
repository
Initial release
Data collection
Database references
Other
1
0
2018-11-28
1
1
2023-06-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_spectrometer.model
Nukacin ISK-1 in active state
N
PDBJ
Y
PDBJ
2018-01-19
REL
REL
REL
REL
THR39, SER41, AND SER48 ARE DEHYDRATED TO DBB39, DAL41 AND DAL48 BY POSTTRANSLATIONAL MODIFICATIONS.
target function
100
20
isotropic
1
2D 1H-1H TOCSY
isotropic
1
2D 1H-1H NOESY
13
mM
natural abundance
34
mM
[U-2H]
10
mM
natural abundance
0
mM
conditions_1
3.5
pH
ambient
Pa
328
K
simulated annealing
1
target function
13 mM nukacin ISK-1, 34 mM [U-2H] dodecylphosphocholine, 10 mM glycine, 90% H2O/10% D2O
natural abundance
90% H2O/10% D2O
micelle
Guntert P.
refinement
CYANA
700
Bruker
AVANCE
LYS
1
n
1
LYS
1
A
LYS
2
n
2
LYS
2
A
LYS
3
n
3
LYS
3
A
SER
4
n
4
SER
4
A
GLY
5
n
5
GLY
5
A
VAL
6
n
6
VAL
6
A
ILE
7
n
7
ILE
7
A
PRO
8
n
8
PRO
8
A
DBB
9
n
9
DBB
9
A
VAL
10
n
10
VAL
10
A
DAL
11
n
11
DAL
11
A
HIS
12
n
12
HIS
12
A
ASP
13
n
13
ASP
13
A
CYS
14
n
14
CYS
14
A
HIS
15
n
15
HIS
15
A
MET
16
n
16
MET
16
A
ASN
17
n
17
ASN
17
A
DAL
18
n
18
DAL
18
A
PHE
19
n
19
PHE
19
A
GLN
20
n
20
GLN
20
A
PHE
21
n
21
PHE
21
A
VAL
22
n
22
VAL
22
A
PHE
23
n
23
PHE
23
A
DBU
24
n
24
DBU
24
A
CYS
25
n
25
CYS
25
A
CYS
26
n
26
CYS
26
A
SER
27
n
27
SER
27
A
author_defined_assembly
1
monomeric
mass spectrometry
0
0
2660
A
DBU
24
modified residue
A
DBU
24
THR
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
identity operation
0.0000000000
0.0000000000
0.0000000000
1
A
A
CB
SG
DAL
CYS
11
25
2.03
1
A
A
CB
SG
DAL
CYS
18
26
2.07
2
A
A
CB
SG
DAL
CYS
18
26
1.87
2
A
A
CB
SG
DAL
CYS
11
25
1.94
3
A
A
CB
SG
DAL
CYS
11
25
1.92
4
A
A
CB
SG
DAL
CYS
11
25
1.89
4
A
A
CB
SG
DAL
CYS
18
26
1.90
5
A
A
CB
SG
DAL
CYS
11
25
1.89
5
A
A
CB
SG
DAL
CYS
18
26
1.90
6
A
A
CB
SG
DAL
CYS
11
25
1.91
7
A
A
CB
SG
DAL
CYS
18
26
1.96
7
A
A
CB
SG
DAL
CYS
11
25
2.03
8
A
A
CB
SG
DAL
CYS
11
25
2.00
8
A
A
CB
SG
DAL
CYS
18
26
2.01
9
A
A
CB
SG
DAL
CYS
11
25
1.92
10
A
A
CB
SG
DAL
CYS
18
26
1.89
10
A
A
CB
SG
DAL
CYS
11
25
1.92
11
A
A
CB
SG
DAL
CYS
11
25
1.91
11
A
A
CB
SG
DAL
CYS
18
26
1.94
12
A
A
CB
SG
DAL
CYS
11
25
1.91
13
A
A
CB
SG
DAL
CYS
11
25
2.01
14
A
A
CB
SG
DAL
CYS
11
25
1.98
14
A
A
CB
SG
DAL
CYS
18
26
2.17
15
A
A
CB
SG
DAL
CYS
11
25
1.94
16
A
A
CB
SG
DAL
CYS
11
25
1.89
17
A
A
CB
SG
DAL
CYS
18
26
1.85
17
A
A
CB
SG
DAL
CYS
11
25
2.11
18
A
A
CB
SG
DAL
CYS
11
25
1.86
18
A
A
CB
SG
DAL
CYS
18
26
1.89
19
A
A
CB
SG
DAL
CYS
18
26
1.92
19
A
A
CB
SG
DAL
CYS
11
25
1.98
20
A
A
CB
SG
DAL
CYS
11
25
1.91
1
A
SER
4
-153.05
48.30
1
A
VAL
6
-177.26
-35.40
1
A
ASP
13
179.00
-32.85
1
A
ASN
17
-51.21
-74.99
1
A
PHE
19
-176.68
137.22
1
A
GLN
20
61.68
-85.82
1
A
VAL
22
33.93
48.54
1
A
PHE
23
179.84
110.83
2
A
LYS
2
-174.36
-44.59
2
A
VAL
6
-149.17
17.64
2
A
DBB
9
89.13
71.01
2
A
HIS
12
-179.37
34.16
2
A
ASP
13
178.96
34.98
2
A
HIS
15
177.62
-50.37
2
A
ASN
17
-112.32
54.70
2
A
PHE
19
174.69
-71.77
2
A
VAL
22
-49.08
102.41
2
A
PHE
23
-177.75
-70.15
2
A
CYS
25
-90.26
41.12
2
A
CYS
26
-143.51
-59.74
3
A
VAL
6
-149.06
17.71
3
A
DBB
9
108.22
70.76
3
A
HIS
12
-141.71
47.28
3
A
ASP
13
-165.10
27.61
3
A
HIS
15
-179.39
-174.97
3
A
MET
16
-117.63
64.92
3
A
ASN
17
-153.52
-45.02
3
A
GLN
20
73.28
-68.42
3
A
VAL
22
37.00
44.60
3
A
CYS
26
-100.76
-64.59
4
A
VAL
6
-149.44
18.03
4
A
DBB
9
99.56
68.97
4
A
DAL
11
66.31
170.11
4
A
HIS
12
-96.85
38.85
4
A
HIS
15
-174.89
-177.87
4
A
ASN
17
-157.77
-41.28
4
A
PHE
19
176.68
-73.15
4
A
GLN
20
-49.41
-76.19
4
A
PHE
23
-177.26
115.54
5
A
VAL
6
-147.14
16.34
5
A
DBB
9
109.38
63.15
5
A
HIS
12
-178.55
133.48
5
A
HIS
15
-156.89
-62.49
5
A
MET
16
-142.09
-75.25
5
A
ASN
17
-179.81
62.26
5
A
PHE
19
-175.84
134.06
5
A
GLN
20
69.66
-72.00
5
A
PHE
21
-97.64
49.47
5
A
PHE
23
-177.02
-65.92
6
A
SER
4
62.00
99.04
6
A
VAL
6
-142.63
24.28
6
A
DBB
9
91.39
71.13
6
A
HIS
12
-179.16
34.24
6
A
ASP
13
-142.28
13.54
6
A
ASN
17
-179.36
-34.60
6
A
PHE
19
62.78
162.27
6
A
GLN
20
65.25
-81.75
6
A
PHE
21
-102.98
51.92
6
A
VAL
22
-65.61
88.93
6
A
PHE
23
-176.96
-69.79
6
A
CYS
25
-92.30
37.09
7
A
SER
4
57.63
-179.49
7
A
ILE
7
-157.74
-61.52
7
A
ASP
13
-176.05
61.88
7
A
CYS
14
-160.71
-35.17
7
A
HIS
15
179.82
-30.66
7
A
PHE
19
64.44
152.40
7
A
GLN
20
67.91
-126.50
7
A
PHE
23
176.44
113.52
8
A
SER
4
-150.25
47.16
8
A
DBB
9
79.93
72.72
8
A
HIS
12
-109.53
42.43
8
A
HIS
15
-175.61
-169.44
8
A
PHE
19
179.88
-81.59
8
A
GLN
20
-59.83
-84.62
8
A
VAL
22
-51.35
94.21
8
A
PHE
23
176.62
118.38
9
A
LYS
2
-163.91
90.78
9
A
SER
4
-171.37
104.02
9
A
VAL
6
-177.67
-32.99
9
A
ASP
13
178.47
35.56
9
A
MET
16
-164.35
-81.38
9
A
ASN
17
177.77
35.14
9
A
DAL
18
106.77
-78.27
9
A
PHE
19
63.33
163.73
9
A
GLN
20
65.56
-81.83
9
A
PHE
21
-107.84
52.81
9
A
VAL
22
-63.28
97.98
9
A
PHE
23
-177.31
111.55
10
A
LYS
3
-134.98
-56.89
10
A
SER
4
52.35
79.36
10
A
ILE
7
-157.83
-61.59
10
A
HIS
12
-153.50
57.83
10
A
ASP
13
-179.44
39.69
10
A
HIS
15
178.52
-37.79
10
A
ASN
17
-111.32
68.79
10
A
PHE
19
-178.31
132.59
10
A
GLN
20
64.98
-78.72
10
A
PHE
23
-171.23
-49.04
10
A
CYS
26
-107.03
77.11
11
A
LYS
2
-95.39
53.95
11
A
VAL
6
-157.76
23.02
11
A
DBB
9
114.55
70.43
11
A
HIS
12
179.32
142.82
11
A
HIS
15
177.69
-168.31
11
A
ASN
17
-148.18
-74.70
11
A
DAL
18
117.10
-62.21
11
A
PHE
19
64.45
-82.47
11
A
GLN
20
-65.72
-113.24
11
A
PHE
23
-177.78
-72.48
11
A
CYS
25
-89.33
38.43
12
A
LYS
2
63.13
163.47
12
A
SER
4
-119.15
77.00
12
A
ASN
17
-168.88
-44.79
12
A
PHE
19
178.99
-68.95
12
A
VAL
22
63.96
84.34
12
A
PHE
23
-176.13
-69.65
13
A
HIS
12
-168.31
28.85
13
A
ASP
13
177.63
33.19
13
A
HIS
15
-176.22
-34.10
13
A
ASN
17
-90.65
47.47
13
A
PHE
19
64.56
167.33
13
A
GLN
20
75.68
-68.95
13
A
VAL
22
37.00
44.16
13
A
PHE
23
-147.22
-71.68
13
A
CYS
25
-91.02
35.81
14
A
LYS
3
-169.25
99.31
14
A
VAL
6
-140.14
25.60
14
A
DBB
9
130.62
73.05
14
A
VAL
10
-104.89
-169.80
14
A
HIS
12
-176.82
51.33
14
A
ASP
13
-178.26
55.65
14
A
CYS
14
-137.67
-46.01
14
A
HIS
15
171.70
-59.18
14
A
ASN
17
-151.57
61.18
14
A
PHE
19
66.01
137.61
14
A
GLN
20
59.69
-90.41
14
A
PHE
23
-155.63
-61.62
15
A
LYS
3
-145.65
33.85
15
A
SER
4
-163.18
108.21
15
A
DAL
11
56.17
-100.89
15
A
HIS
15
171.40
118.81
15
A
MET
16
50.49
-168.39
15
A
ASN
17
-102.66
68.68
15
A
PHE
19
-169.97
-81.74
15
A
PHE
21
-167.47
27.70
15
A
PHE
23
-163.18
-71.21
16
A
VAL
6
-141.92
26.10
16
A
DBB
9
104.56
70.56
16
A
HIS
12
-175.80
32.88
16
A
ASP
13
-143.56
14.38
16
A
HIS
15
-177.24
-177.77
16
A
MET
16
-105.24
-167.48
16
A
ASN
17
73.37
-68.38
16
A
GLN
20
75.67
-69.06
16
A
VAL
22
35.26
79.83
16
A
PHE
23
-162.79
-71.89
16
A
CYS
25
-160.74
-39.37
17
A
PRO
8
-69.78
-72.43
17
A
DBB
9
143.46
66.55
17
A
DAL
11
51.09
-104.08
17
A
HIS
12
-157.76
73.10
17
A
ASP
13
-135.09
-37.31
17
A
CYS
14
-78.57
-77.80
17
A
MET
16
62.66
161.61
17
A
PHE
19
-179.43
-79.24
17
A
VAL
22
65.46
127.27
17
A
PHE
23
179.61
-72.72
17
A
CYS
25
-160.67
-72.48
17
A
CYS
26
-165.70
-80.71
18
A
VAL
6
-153.50
24.77
18
A
DBB
9
137.62
72.16
18
A
VAL
10
-121.75
-73.85
18
A
DAL
11
-55.54
176.09
18
A
HIS
12
-67.59
85.87
18
A
ASP
13
-156.46
-41.39
18
A
CYS
14
-92.50
-81.66
18
A
PHE
19
-176.79
133.32
18
A
GLN
20
69.52
-72.18
18
A
PHE
21
-97.86
45.07
18
A
PHE
23
-176.39
-68.82
19
A
LYS
2
59.30
177.29
19
A
ILE
7
-157.82
-61.51
19
A
HIS
12
61.65
103.48
19
A
ASP
13
-179.15
-42.08
19
A
CYS
14
-95.92
-73.41
19
A
GLN
20
73.73
-59.48
19
A
PHE
21
-107.51
-69.03
19
A
VAL
22
62.61
107.22
19
A
PHE
23
-165.15
-50.63
20
A
LYS
2
61.25
169.44
20
A
ASP
13
74.67
-59.59
20
A
HIS
15
178.35
149.11
20
A
MET
16
-112.26
78.20
20
A
ASN
17
179.34
-33.16
20
A
PHE
19
-159.24
-81.79
20
A
PHE
21
-100.71
59.40
20
A
PHE
23
-178.74
-70.71
N
Nukacin ISK-1 in active state
1
N
N
covale
1.329
one
A
PRO
8
A
C
PRO
8
1_555
A
DBB
9
A
N
DBB
9
1_555
covale
1.329
both
A
DBB
9
A
C
DBB
9
1_555
A
VAL
10
A
N
VAL
10
1_555
covale
1.942
none
A
DBB
9
A
CB
DBB
9
1_555
A
CYS
14
A
SG
CYS
14
1_555
covale
1.329
both
A
VAL
10
A
C
VAL
10
1_555
A
DAL
11
A
N
DAL
11
1_555
covale
1.329
both
A
DAL
11
A
C
DAL
11
1_555
A
HIS
12
A
N
HIS
12
1_555
covale
1.329
both
A
ASN
17
A
C
ASN
17
1_555
A
DAL
18
A
N
DAL
18
1_555
covale
1.329
both
A
DAL
18
A
C
DAL
18
1_555
A
PHE
19
A
N
PHE
19
1_555
covale
1.329
both
A
PHE
23
A
C
PHE
23
1_555
A
DBU
24
A
N
DBU
24
1_555
covale
1.328
both
A
DBU
24
A
C
DBU
24
1_555
A
CYS
25
A
N
CYS
25
1_555
ANTIBIOTIC
lantibiotics, ANTIBIOTIC
LANNA_STAWA
UNP
1
31
Q9KWM4
KKKSGVIPTVSHDCHMNSFQFVFTCCS
31
57
5Z5Q
1
27
Q9KWM4
A
1
1
27
1
THR
see sequence details
DBB
9
5Z5Q
A
Q9KWM4
UNP
39
9
1
SER
see sequence details
DAL
11
5Z5Q
A
Q9KWM4
UNP
41
11
1
SER
see sequence details
DAL
18
5Z5Q
A
Q9KWM4
UNP
48
18