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
4441.817
BACTERIOCIN SAKACIN P
1
man
polymer
SAKACIN 674
no
no
KYYGNGVHCGKHSCTVDWGTAIGNIGNNAAANWATGGNAGWNK
KYYGNGVHCGKHSCTVDWGTAIGNIGNNAAANWATGGNAGWNK
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
LB790
sample
1599
LACTOBACILLUS SAKE
LB790/PMLS114
1599
LACTOBACILLUS SAKE
LB790
LB790/PMLS114
PMG36E
PMLS114
repository
Initial release
Version format compliance
Version format compliance
1
0
2003-09-22
1
1
2011-05-08
1
2
2011-07-13
SAKACIN P VARIANT THAT IS STRUCTURALLY STABILIZED BY AN INSERTED C-TERMINAL DISULFIDE BRIDGE.
THREE-DIMENSIONAL STRUCTURE IN LIPID MICELLES OF THE PEDIOCIN-LIKE ANTIMICROBIAL PEPTIDE SAKACIN P.
PDBE
Y
PDBE
2003-04-25
REL
BACTERICIDAL ACTIVITY; INHIBITS LISTERIA AND MANY
LACTOBACILLI SPECIES.
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
90% TFE,0.1% TFA, 10% D2O,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
600
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
ASN
24
n
24
ASN
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
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
TYR
3
A
N
TYR
3
A
O
VAL
7
A
O
VAL
7
1
A
A
HIS
SER
12
13
-149.01
1
A
A
CYS
THR
14
15
-145.32
1
A
A
ALA
ASN
31
32
127.23
1
A
A
TRP
ALA
33
34
137.42
3
A
A
VAL
ASP
16
17
129.11
3
A
A
ASP
TRP
17
18
-148.77
3
A
A
ASN
ASN
27
28
145.66
4
A
A
GLY
VAL
6
7
-146.75
4
A
A
ALA
ASN
31
32
132.24
6
A
A
SER
CYS
13
14
-143.08
6
A
A
ALA
ALA
30
31
148.79
6
A
A
GLY
ASN
37
38
-146.35
9
A
A
ALA
ASN
31
32
142.25
9
A
A
ASN
TRP
32
33
147.44
10
A
A
ALA
ALA
30
31
148.05
3
A
TYR
3
0.080
SIDE CHAIN
4
A
TYR
2
0.075
SIDE CHAIN
4
A
TYR
3
0.084
SIDE CHAIN
5
A
TYR
2
0.087
SIDE CHAIN
2
11.88
1.90
113.70
125.58
A
A
A
CA
CB
CG
TRP
TRP
TRP
18
18
18
N
4
-6.05
0.60
121.00
114.95
A
A
A
CB
CG
CD2
TYR
TYR
TYR
2
2
2
N
4
3.74
0.60
121.00
124.74
A
A
A
CB
CG
CD1
TYR
TYR
TYR
2
2
2
N
6
8.36
1.10
114.20
122.56
A
A
A
CA
CB
SG
CYS
CYS
CYS
9
9
9
N
1
A
ASN
5
48.17
-87.01
1
A
LYS
11
-143.66
-39.96
1
A
CYS
14
-45.51
94.01
1
A
VAL
16
63.79
-70.70
1
A
ASP
17
-173.77
-6.35
1
A
TRP
33
65.73
-30.68
1
A
ALA
34
-59.68
-9.65
1
A
THR
35
80.79
69.67
2
A
TYR
3
100.56
-82.32
2
A
ASN
5
31.70
73.60
2
A
HIS
12
-143.16
37.43
2
A
CYS
14
71.40
74.38
2
A
THR
15
-59.13
173.40
2
A
THR
35
-124.62
-79.15
3
A
ASN
5
26.28
-91.45
3
A
HIS
12
-136.70
-54.43
3
A
ALA
34
-146.25
-16.57
4
A
TYR
2
-67.03
-95.54
4
A
ASN
5
-136.85
-54.38
4
A
VAL
7
-53.02
-95.85
4
A
HIS
8
106.60
23.99
4
A
HIS
12
-153.75
67.73
4
A
THR
15
-64.16
97.41
4
A
ASP
17
120.97
-25.89
4
A
TRP
18
-62.90
22.10
4
A
ALA
30
-56.30
-9.22
4
A
THR
35
-132.08
-52.71
5
A
TYR
2
-83.24
-123.98
5
A
TYR
3
47.72
-16.51
5
A
ASN
5
38.14
68.07
5
A
VAL
7
58.84
167.60
5
A
HIS
12
-151.94
-71.38
5
A
CYS
14
-74.81
36.67
5
A
VAL
16
52.01
19.95
5
A
ASP
17
49.99
16.34
5
A
ASN
38
54.81
-77.93
5
A
TRP
41
-59.96
97.48
6
A
LYS
11
-133.49
-56.97
6
A
HIS
12
-74.91
-152.34
6
A
VAL
16
-69.81
28.22
6
A
ASP
17
55.92
-2.60
6
A
TRP
33
28.47
-66.65
6
A
THR
35
-148.84
44.61
6
A
ASN
38
44.72
-40.03
6
A
ASN
42
-68.53
82.17
7
A
HIS
8
48.98
78.55
7
A
SER
13
-85.34
-92.11
7
A
VAL
16
45.67
-110.81
7
A
ALA
34
-146.04
-24.28
8
A
ASN
5
40.74
-92.64
8
A
SER
13
-102.49
62.12
8
A
CYS
14
65.74
-38.30
8
A
THR
15
59.17
-81.92
8
A
VAL
16
57.67
-5.70
8
A
ASP
17
59.25
18.20
8
A
THR
35
-138.24
-71.28
8
A
ASN
42
48.81
19.62
9
A
LYS
11
66.23
-53.72
9
A
ASP
17
-176.43
-42.41
9
A
TRP
18
-79.67
22.46
9
A
TRP
33
32.63
-72.56
9
A
THR
35
-149.72
-25.19
9
A
ASN
38
-121.88
-86.67
10
A
VAL
7
-141.79
-60.72
10
A
HIS
8
51.13
-77.43
10
A
CYS
9
64.38
-47.20
10
A
HIS
12
-162.29
-53.03
10
A
CYS
14
-65.94
76.15
10
A
VAL
16
58.35
-46.76
10
A
ASP
17
126.76
-3.37
10
A
ALA
30
-59.11
-9.30
10
A
ALA
31
-111.11
-71.03
10
A
ALA
34
-144.76
-23.72
10
A
THR
35
-133.82
-37.35
BACTERIOCIN SAKACIN P
Three-dimensional structure in lipid micelles of the pediocin-like antimicrobial peptide sakacin P.
1
N
N
A
TRP
18
A
TRP
18
HELX_P
A
TRP
33
A
TRP
33
1
1
16
disulf
2.034
A
CYS
9
A
SG
CYS
9
1_555
A
CYS
14
A
SG
CYS
14
1_555
ANTIBIOTIC
PEDIOCIN-LIKE BACTERIOCINS, ANTIMICROBIAL PEPTIDES, SAKACIN P, ANTIBIOTIC
A
ASN
5
A
ASN
5
2
A
GLY
6
A
GLY
6
-9.16
A
TYR
3
A
TYR
3
4
A
GLY
4
A
GLY
4
4.17
A
ASN
5
A
ASN
5
7
A
GLY
6
A
GLY
6
-7.33
A
GLY
36
A
GLY
36
7
A
GLY
37
A
GLY
37
-7.69
SAKP_LACSK
UNP
1
P35618
19
61
1OG7
1
43
P35618
A
1
1
43
2
anti-parallel
A
TYR
2
A
TYR
2
A
GLY
4
A
GLY
4
A
VAL
7
A
VAL
7
A
HIS
8
A
HIS
8
1
P 1