1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Cameron, A.J.
Ewdards, P.J.B.
Harjes, E.
Sarojini, V.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C7 H7 N O2
137.136
2-AMINOBENZOIC ACID
L-peptide linking
C9 H11 N O2
165.189
D-PHENYLALANINE
D-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
C5 H12 N2 O2
132.161
n
L-ornithine
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
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
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
C
N
7
N
O
N
8
N
N
N
9
N
O
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
C
N
19
N
O
N
20
N
O
Y
21
N
C
Y
22
N
C
Y
23
N
C
N
24
N
N
Y
25
N
C
Y
26
N
C
Y
27
N
C
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
N
N
36
R
C
N
37
N
C
N
38
N
O
N
39
N
O
N
40
N
C
Y
41
N
C
Y
42
N
C
Y
43
N
C
Y
44
N
C
Y
45
N
C
Y
46
N
C
N
47
N
H
N
48
N
H
N
49
N
H
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
C
N
65
N
C
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
N
N
81
S
C
N
82
N
C
N
83
N
O
N
84
N
C
N
85
N
C
N
86
N
C
N
87
N
C
N
88
N
N
N
89
N
O
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
N
N
106
S
C
N
107
N
C
N
108
N
C
N
109
N
C
N
110
N
N
N
111
N
C
N
112
N
O
N
113
N
O
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
N
N
127
S
C
N
128
N
C
N
129
N
O
N
130
N
C
Y
131
N
C
Y
132
N
C
Y
133
N
C
Y
134
N
C
Y
135
N
C
Y
136
N
C
N
137
N
O
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
N
N
150
S
C
N
151
N
C
N
152
N
O
N
153
N
C
Y
154
N
C
Y
155
N
C
Y
156
N
C
Y
157
N
C
Y
158
N
C
Y
159
N
C
N
160
N
O
N
161
N
O
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
N
N
174
S
C
N
175
N
C
N
176
N
O
N
177
N
C
N
178
N
C
N
179
N
C
N
180
N
O
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
doub
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
doub
N
18
N
sing
N
19
N
sing
N
20
N
sing
Y
21
N
doub
Y
22
N
sing
Y
23
N
sing
N
24
N
sing
Y
25
N
doub
N
26
N
sing
N
27
N
sing
N
28
N
sing
Y
29
N
sing
N
30
N
sing
Y
31
N
doub
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
doub
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
Y
46
N
doub
Y
47
N
sing
Y
48
N
sing
N
49
N
sing
Y
50
N
doub
N
51
N
sing
Y
52
N
doub
N
53
N
sing
Y
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
sing
N
62
N
sing
N
63
N
doub
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
doub
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
doub
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
doub
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
Y
133
N
doub
Y
134
N
sing
Y
135
N
sing
N
136
N
sing
Y
137
N
doub
N
138
N
sing
Y
139
N
doub
N
140
N
sing
Y
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
doub
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
Y
156
N
doub
Y
157
N
sing
Y
158
N
sing
N
159
N
sing
Y
160
N
doub
N
161
N
sing
Y
162
N
doub
N
163
N
sing
Y
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
doub
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
US
J. Med. Chem.
JMCMAR
0151
1520-4804
60
9565
9574
10.1021/acs.jmedchem.7b00953
29140694
Tyrocidine A Analogues Bearing the Planar d-Phe-2-Abz Turn Motif: How Conformation Impacts Bioactivity.
2017
10.2210/pdb6b35/pdb
pdb_00006b35
1311.548
Tyrocidine A analogue D-PHE-BE2-PHE-D-PHE-ASN-LYS-TYR-VAL-ORN-LEU
1
syn
polymer
no
yes
(DPN)(BE2)F(DPN)NKYV(ORN)L
FXFFNKYVAL
A
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
citation
atom_site
pdbx_molecule_features
pdbx_nmr_spectrometer
struct_conn
database_2
pdbx_database_status
atom_site
chem_comp_atom
chem_comp_bond
pdbx_validate_rmsd_angle
pdbx_validate_torsion
struct_conn
repository
Initial release
Database references
Atomic model
Data collection
Derived calculations
Structure summary
Database references
Other
Atomic model
Data collection
Derived calculations
1
0
2017-12-06
1
1
2017-12-27
2
0
2020-08-12
2
1
2023-06-14
3
0
2023-11-15
_citation.journal_volume
_citation.page_first
_citation.page_last
_atom_site.auth_atom_id
_atom_site.label_atom_id
_pdbx_nmr_spectrometer.model
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_atom_site.auth_atom_id
_atom_site.label_atom_id
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr2_label_atom_id
NMR ensemble of Tyrocidine A analogue AC3.28
N
RCSB
Y
RCSB
2017-09-20
REL
REL
REL
REL
Synthetic analogue of tyrocidine A. Sequence is altered at 2 positions relative to natural product.
1393
Brevibacillus brevis
sample
1
10
Tyrocidine kills bacteria by interacting with their cytoplasmic membrane and causing leakage of their intracellular content. It also affects intracellular membranes such as those of mitochondria
Antibiotic
Tyrocidine A analogue (DPN)(BE2)F(DPN)NKYV(ORN)L
Cyclic peptide
structures with acceptable covalent geometry
10
8
isotropic
1
2D 1H-15N HSQC
isotropic
1
2D 1H-1H TOCSY
isotropic
1
2D 1H-1H COSY
isotropic
1
2D 1H-1H NOESY
0.8
mM
None
0
Not defined
conditions_1
6
2
pH
1
atm
298
K
simulated annealing
1
lowest energy
0.8 mM None D-PHE-ABZ-PHE-D-PHE-ASN-LYS-TYR-VAL-ORN-LEU, 50% H20 /50% MeCN
AC3.28
50% H20 /50% MeCN
solution
E.KRIGER
refinement
YASARA
structure solution
ANALYSIS
700
Bruker
AVANCE
DPN
1
n
1
DPN
1
A
BE2
2
n
2
BE2
2
A
PHE
3
n
3
PHE
3
A
DPN
4
n
4
DPN
4
A
ASN
5
n
5
ASN
5
A
LYS
6
n
6
LYS
6
A
TYR
7
n
7
TYR
7
A
VAL
8
n
8
VAL
8
A
ORN
9
n
9
ORN
9
A
LEU
10
n
10
LEU
10
A
author_defined_assembly
1
monomeric
none
220
1
1430
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
27.06
2.20
117.20
144.26
A
A
A
CA
C
N
BE2
BE2
PHE
2
2
3
Y
2
27.21
2.20
117.20
144.41
A
A
A
CA
C
N
BE2
BE2
PHE
2
2
3
Y
3
25.95
2.20
117.20
143.15
A
A
A
CA
C
N
BE2
BE2
PHE
2
2
3
Y
4
27.33
2.20
117.20
144.53
A
A
A
CA
C
N
BE2
BE2
PHE
2
2
3
Y
5
26.83
2.20
117.20
144.03
A
A
A
CA
C
N
BE2
BE2
PHE
2
2
3
Y
6
26.58
2.20
117.20
143.78
A
A
A
CA
C
N
BE2
BE2
PHE
2
2
3
Y
7
26.42
2.20
117.20
143.62
A
A
A
CA
C
N
BE2
BE2
PHE
2
2
3
Y
8
26.35
2.20
117.20
143.55
A
A
A
CA
C
N
BE2
BE2
PHE
2
2
3
Y
1
A
DPN
4
-85.34
-127.87
1
A
ASN
5
-125.17
-163.53
2
A
BE2
2
-175.55
-178.89
2
A
DPN
4
-85.00
-124.14
3
A
BE2
2
172.88
-166.88
3
A
DPN
4
-85.06
-128.74
4
A
BE2
2
-173.37
-174.11
4
A
DPN
4
-85.14
-119.86
4
A
LYS
6
-67.21
0.57
5
A
DPN
4
-85.47
-123.16
6
A
DPN
4
-84.88
-138.38
7
A
BE2
2
-176.53
-180.00
7
A
DPN
4
-85.32
-122.05
8
A
DPN
4
-84.82
-105.30
8
A
TYR
7
-126.92
-51.12
N
NMR ensemble of Tyrocidine A analogue AC3.28
1
N
N
covale
1.396
both
A
DPN
1
A
C
DPN
1
1_555
A
BE2
2
A
N
BE2
2
1_555
covale
1.335
both
A
DPN
1
A
N
DPN
1
1_555
A
LEU
10
A
C
LEU
10
1_555
covale
1.383
both
A
BE2
2
A
C
BE2
2
1_555
A
PHE
3
A
N
PHE
3
1_555
covale
1.333
both
A
PHE
3
A
C
PHE
3
1_555
A
DPN
4
A
N
DPN
4
1_555
covale
1.323
both
A
DPN
4
A
C
DPN
4
1_555
A
ASN
5
A
N
ASN
5
1_555
covale
1.334
both
A
VAL
8
A
C
VAL
8
1_555
A
ORN
9
A
N
ORN
9
1_555
covale
1.338
both
A
ORN
9
A
C
ORN
9
1_555
A
LEU
10
A
N
LEU
10
1_555
ANTIMICROBIAL PROTEIN
Tyrocidine A Antimicrobial peptide AMP Cyclic peptide 2-aminobenzoic acid 2-Abz Anthranilic acid, ANTIMICROBIAL PROTEIN
6B35
PDB
1
1
6B35
1
10
6B35
1
10
6B35
A
1
1
10