1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Uteng, M.
Hauge, H.H.
Markwick, P.R.
Fimland, G.
Mantzilas, D.
Nissen-Meyer, J.
Muhle-Goll, C.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C3 H7 N O2
89.093
y
ALANINE
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
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
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Biochemistry
BICHAW
0033
0006-2960
42
11417
10.1021/BI034572I
14516192
Three-Dimensional Structure in Lipid Micelles of the Pediocin-Like Antimicrobial Peptide Sakacin P and a Sakacin P Variant that is Structurally Stabilized by an Inserted C-Terminal Disulfide Bridge
2003
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
SAKACIN P VARIANT THAT IS STRUCTURALLY STABILIZED BY AN INSERTED C-TERMINAL DISULFIDE BRIDGE.
4534.000
BACTERIOCIN SAKACIN P
YES
1
man
polymer
SAKACIN 674
no
no
KYYGNGVHCGKHSCTVDWGTAIGCIGNNAAANWATGGNAGWNKC
KYYGNGVHCGKHSCTVDWGTAIGCIGNNAAANWATGGNAGWNKC
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
LB790
sample
1599
LACTOBACILLUS SAKE
LB790/PGF10
1599
LACTOBACILLUS SAKE
LB790
LB790/PGF10
PMG36E
PGF10
repository
Initial release
Version format compliance
Version format compliance
1
0
2003-09-22
1
1
2011-05-08
1
2
2011-07-13
THREE-DIMENSIONAL STRUCTURE IN LIPID MICELLES OF THE PEDIOCIN-LIKE ANTIMICROBIAL PEPTIDE SAKACIN P.
THREE-DIMENSIONAL STRUCTURE IN LIPID MICELLES OF THE PEDIOCIN-LIKE ANTIMICROBIAL PEPTIDE SAKACIN P.
PDBE
Y
PDBE
2003-05-28
REL
ENGINEERED MUTATION IN CHAIN A: CYS 42 TO ASN 42
SAKACIN P VARIANT THAT IS STRUCTURALLY STABILIZED BY AN
INSERTED C-TERMINAL DISULFIDE BRIDGE.
THE SEQUENCE IS DESCRIBED IN J. BACTERIOL. 182, 2643-2648
THE STRUCTURES WERE DETERMINED USING A COMBINATION OF 1H NMR SPECTROSCOPIC METHODS FOLLOWED BY DISTANCE GEOMETRY/SIMULATED ANNEALING CALCULATIONS.
LEAST RESTRAIN VIOLATION AND OVERALL ENERGY
50
10
NOESY TOCSY
2.8
pH
298
K
AMBER 6, SAN FRANCISCO, UNIVERSITY OF CALIFORNIA, 1999.
MOLECULAR DYNAMICS/ SIMULATED ANNEALING
1
250 MM DPC/10% D2O/ 0.1% TFA/1MM PEPTIDE
CASE, D.A., PEARLMAN, D.A., CALDWELL, III, J.C., ET AL.
refinement
AMBER
6
structure solution
ARIA
structure solution
AMBER
500
Bruker
DRX
LYS
1
n
1
LYS
1
A
TYR
2
n
2
TYR
2
A
TYR
3
n
3
TYR
3
A
GLY
4
n
4
GLY
4
A
ASN
5
n
5
ASN
5
A
GLY
6
n
6
GLY
6
A
VAL
7
n
7
VAL
7
A
HIS
8
n
8
HIS
8
A
CYS
9
n
9
CYS
9
A
GLY
10
n
10
GLY
10
A
LYS
11
n
11
LYS
11
A
HIS
12
n
12
HIS
12
A
SER
13
n
13
SER
13
A
CYS
14
n
14
CYS
14
A
THR
15
n
15
THR
15
A
VAL
16
n
16
VAL
16
A
ASP
17
n
17
ASP
17
A
TRP
18
n
18
TRP
18
A
GLY
19
n
19
GLY
19
A
THR
20
n
20
THR
20
A
ALA
21
n
21
ALA
21
A
ILE
22
n
22
ILE
22
A
GLY
23
n
23
GLY
23
A
CYS
24
n
24
CYS
24
A
ILE
25
n
25
ILE
25
A
GLY
26
n
26
GLY
26
A
ASN
27
n
27
ASN
27
A
ASN
28
n
28
ASN
28
A
ALA
29
n
29
ALA
29
A
ALA
30
n
30
ALA
30
A
ALA
31
n
31
ALA
31
A
ASN
32
n
32
ASN
32
A
TRP
33
n
33
TRP
33
A
ALA
34
n
34
ALA
34
A
THR
35
n
35
THR
35
A
GLY
36
n
36
GLY
36
A
GLY
37
n
37
GLY
37
A
ASN
38
n
38
ASN
38
A
ALA
39
n
39
ALA
39
A
GLY
40
n
40
GLY
40
A
TRP
41
n
41
TRP
41
A
ASN
42
n
42
ASN
42
A
LYS
43
n
43
LYS
43
A
CYS
44
n
44
CYS
44
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
1
A
A
VAL
ASP
16
17
138.76
1
A
A
ASN
LYS
42
43
-92.42
2
A
A
THR
GLY
35
36
147.79
2
A
A
ASN
LYS
42
43
139.93
3
A
A
VAL
ASP
16
17
119.72
3
A
A
ASN
TRP
32
33
-137.71
3
A
A
THR
GLY
35
36
143.80
3
A
A
ASN
LYS
42
43
141.24
5
A
A
ASN
LYS
42
43
-114.84
6
A
A
CYS
THR
14
15
-148.78
6
A
A
VAL
ASP
16
17
143.77
6
A
A
ASN
TRP
32
33
-129.59
7
A
A
VAL
ASP
16
17
141.02
7
A
A
GLY
GLY
36
37
142.57
7
A
A
ASN
LYS
42
43
-141.74
7
A
A
LYS
CYS
43
44
125.05
8
A
A
VAL
ASP
16
17
118.74
8
A
A
ASN
TRP
32
33
-147.90
8
A
A
THR
GLY
35
36
148.21
8
A
A
GLY
GLY
36
37
146.91
9
A
A
THR
GLY
35
36
147.12
9
A
A
ASN
LYS
42
43
-104.84
10
A
A
CYS
THR
14
15
-138.72
10
A
A
THR
VAL
15
16
-149.10
10
A
A
LYS
CYS
43
44
-124.87
2
A
HIS
8
0.091
SIDE CHAIN
1
8.35
1.10
114.20
122.55
A
A
A
CA
CB
SG
CYS
CYS
CYS
9
9
9
N
2
7.46
1.20
111.50
118.96
A
A
A
CB
CA
C
CYS
CYS
CYS
9
9
9
N
5
15.86
2.50
121.70
137.56
A
A
A
C
N
CA
THR
VAL
VAL
15
16
16
Y
9
15.35
2.50
121.70
137.05
A
A
A
C
N
CA
GLY
ASN
ASN
37
38
38
Y
10
15.41
2.50
121.70
137.11
A
A
A
C
N
CA
HIS
SER
SER
12
13
13
Y
10
10.37
1.50
110.90
121.27
A
A
A
CA
CB
CG1
VAL
VAL
VAL
16
16
16
N
1
A
VAL
7
51.39
150.04
1
A
CYS
9
-153.93
-128.63
1
A
SER
13
172.62
-44.97
1
A
CYS
14
-74.42
-74.01
1
A
THR
15
52.89
-127.44
1
A
VAL
16
48.82
95.51
1
A
ALA
29
-56.79
-72.97
1
A
TRP
33
-178.63
-126.04
1
A
THR
35
-158.23
57.95
1
A
ASN
38
-153.62
7.30
1
A
ALA
39
52.63
19.98
1
A
ASN
42
-164.52
3.72
2
A
CYS
9
144.20
-175.23
2
A
LYS
11
-56.53
-5.24
2
A
TRP
18
-68.88
23.45
2
A
CYS
24
-52.96
-73.45
2
A
TRP
33
175.59
-135.24
2
A
THR
35
139.51
86.84
2
A
ASN
42
-53.25
-2.24
3
A
CYS
14
61.41
81.82
3
A
VAL
16
-14.31
112.11
3
A
TRP
33
172.92
-122.30
3
A
ALA
34
-145.13
-34.15
3
A
ALA
39
-76.88
20.30
3
A
ASN
42
-57.14
2.25
4
A
VAL
7
49.60
-95.96
4
A
HIS
8
97.07
99.11
4
A
LYS
11
61.46
-26.33
4
A
SER
13
172.47
-169.67
4
A
THR
15
-142.86
-133.81
4
A
VAL
16
-146.19
-1.19
4
A
ASP
17
102.34
-18.23
4
A
TRP
18
-154.04
7.92
4
A
CYS
24
-55.74
-74.08
4
A
TRP
33
146.04
-101.61
4
A
ALA
34
-154.84
43.49
4
A
THR
35
56.09
79.86
4
A
ASN
42
147.49
8.26
4
A
LYS
43
1.28
82.38
5
A
TYR
3
-34.77
114.60
5
A
ASN
5
-141.07
-6.79
5
A
HIS
8
-156.89
89.11
5
A
HIS
12
-116.13
-124.69
5
A
CYS
14
-128.32
-66.39
5
A
THR
15
54.04
-174.78
5
A
ALA
29
-55.61
-72.67
5
A
TRP
33
-153.35
-55.46
5
A
ASN
38
-144.05
-48.62
5
A
ALA
39
58.90
-26.36
5
A
ASN
42
-162.77
0.18
5
A
LYS
43
-27.81
138.95
6
A
TYR
2
85.46
95.06
6
A
TYR
3
-135.21
-69.06
6
A
VAL
7
-20.84
136.20
6
A
HIS
12
-102.35
-82.91
6
A
CYS
14
54.28
92.68
6
A
THR
15
-121.64
-55.78
6
A
TRP
18
-53.47
-6.28
6
A
TRP
33
157.86
-118.05
6
A
THR
35
118.84
100.49
6
A
ASN
42
149.66
25.34
6
A
LYS
43
-24.34
108.21
7
A
ASN
5
-118.29
-77.95
7
A
HIS
8
33.57
77.64
7
A
CYS
9
-102.35
-86.20
7
A
CYS
14
-66.12
-87.00
7
A
THR
15
61.01
-60.25
7
A
TRP
33
147.26
-106.33
7
A
ALA
34
-165.00
-33.99
7
A
ASN
42
-152.51
12.29
7
A
LYS
43
46.77
173.13
8
A
ASN
5
-63.39
10.57
8
A
LYS
11
-72.01
40.97
8
A
HIS
12
-131.32
-118.20
8
A
CYS
14
62.95
86.71
8
A
CYS
24
-56.48
-70.20
8
A
TRP
33
170.80
-113.43
8
A
ALA
34
-154.19
-39.04
8
A
ASN
42
153.13
20.28
8
A
LYS
43
-15.05
94.50
9
A
ASN
5
59.84
-22.91
9
A
HIS
12
-116.33
-87.70
9
A
CYS
14
65.66
158.97
9
A
TRP
18
101.18
-54.33
9
A
TRP
33
175.51
-123.83
9
A
ASN
38
127.63
-32.30
9
A
ALA
39
-159.11
-4.55
9
A
ASN
42
170.57
21.70
9
A
LYS
43
-32.99
103.13
10
A
VAL
7
-46.50
157.75
10
A
SER
13
-84.30
-71.46
10
A
ASP
17
132.36
-47.23
10
A
TRP
33
141.12
-105.38
10
A
THR
35
102.56
66.20
10
A
ASN
42
-152.20
7.08
10
A
LYS
43
62.95
-27.31
BACTERIOCIN SAKACIN P
Sakacin P variant that is structurally stabilized by an inserted C-terminal disulfide bridge.
1
N
N
A
TRP
18
A
TRP
18
HELX_P
A
TRP
33
A
TRP
33
1
1
16
disulf
2.009
A
CYS
9
A
SG
CYS
9
1_555
A
CYS
14
A
SG
CYS
14
1_555
disulf
2.048
A
CYS
24
A
SG
CYS
24
1_555
A
CYS
44
A
SG
CYS
44
1_555
ANTIBIOTIC
ANTIBIOTIC, PEDIOCIN-LIKE BACTERIOCINS, ANTIMICROBIAL PEPTIDES, SAKACIN ANTIBIOTIC, BACTERIOCIN
A
CYS
9
A
CYS
9
2
A
GLY
10
A
GLY
10
10.04
A
THR
15
A
THR
15
5
A
VAL
16
A
VAL
16
4.27
A
ASN
32
A
ASN
32
5
A
TRP
33
A
TRP
33
2.79
A
HIS
12
A
HIS
12
10
A
SER
13
A
SER
13
5.93
SAKP_LACSK
UNP
1
P35618
1OHM
PDB
1
1OHM
19
61
1OHM
1
43
P35618
A
1
1
43
44
44
1OHM
44
44
1OHM
A
2
44
44
1
ASN
engineered mutation
CYS
24
1OHM
A
P35618
UNP
42
24
1
insertion
CYS
44
1OHM
A
1OHM
PDB
44
1
P 1