1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Sham, S.S.
Townsley, L.E.
Hinton, J.F.
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
C6 H13 N O2
131.173
D-LEUCINE
D-peptide linking
C5 H11 N O2
117.146
D-VALINE
D-peptide linking
C2 H7 N O
61.083
ETHANOLAMINE
L-peptide COOH carboxy terminus
C6 H11 N O3
145.156
n
N-formyl-L-valine
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
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
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
R
C
N
16
N
C
N
17
N
C
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
O
N
22
N
O
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
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
H
N
36
N
N
N
37
R
C
N
38
N
C
N
39
N
C
N
40
N
C
N
41
N
C
N
42
N
O
N
43
N
O
N
44
N
H
N
45
N
H
N
46
N
H
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
C
N
56
N
N
N
57
N
C
N
58
N
O
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
H
N
64
N
H
N
65
N
H
N
66
N
C
N
67
N
N
N
68
N
O
N
69
S
C
N
70
N
C
N
71
N
C
N
72
N
C
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
H
N
81
N
H
N
82
N
O
N
83
N
C
N
84
N
H
N
85
N
O
N
86
N
H
N
87
N
N
N
88
N
C
N
89
N
C
N
90
N
O
N
91
N
O
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
N
H
N
97
N
N
N
98
S
C
N
99
N
C
N
100
N
O
N
101
N
C
Y
102
N
C
Y
103
N
C
Y
104
N
C
Y
105
N
N
Y
106
N
C
Y
107
N
C
Y
108
N
C
Y
109
N
C
Y
110
N
C
N
111
N
O
N
112
N
H
N
113
N
H
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
N
N
125
S
C
N
126
N
C
N
127
N
O
N
128
N
C
N
129
N
C
N
130
N
C
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
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
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
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
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
doub
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
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
doub
N
63
N
sing
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
doub
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
doub
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
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
Y
102
N
doub
Y
103
N
sing
Y
104
N
sing
N
105
N
sing
Y
106
N
doub
Y
107
N
sing
Y
108
N
sing
N
109
N
sing
Y
110
N
sing
Y
111
N
doub
N
112
N
sing
Y
113
N
doub
N
114
N
sing
Y
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
doub
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
US
Biochemistry
BICHAW
0033
0006-2960
42
1401
10.1021/BI0204286
12578352
The Structure, Cation Binding, Transport and Conductance of Gly15-Gramicidin a Incorporated Into Sds Micelles and Pc/Pg Vesicles
2003
10.2210/pdb1ng8/pdb
pdb_00001ng8
1.000000
0.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
x-ray
1
1.0
1753.136
GRAMICIDIN A
2
syn
polymer
VALYL GRAMICIDIN
no
yes
(FVA)GA(DLE)A(DVA)V(DVA)W(DLE)W(DLE)W(DLE)G(ETA)
VGALAVVVWLWLWLGX
A,B
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
atom_site
chem_comp_atom
chem_comp_bond
database_2
struct_conn
struct_ref_seq_dif
repository
Initial release
Version format compliance
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Other
Other
Atomic model
Data collection
Database references
Derived calculations
1
0
2002-12-31
1
1
2011-06-14
1
2
2011-07-13
1
3
2011-07-27
1
4
2012-12-12
1
5
2013-07-02
2
0
2023-11-15
_atom_site.auth_atom_id
_atom_site.label_atom_id
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_ref_seq_dif.details
CRYSTAL STRUCTURE OF GRAMICIDIN S COMPLEXED WITH ALKALINE PROTEINASE SAVINASE
CRYSTAL STRUCTURE OF GRAMICIDIN A FROM CRYSTALS GROWN IN A LIPID CUBIC PHASE.
CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE
CRYSTAL STRUCTURE OF GRAMICIDIN A FROM BACILLUS BREVIS
CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLEXED WITH CESIUM CHLORIDE
CRYSTAL STRUCTURE OF GRAMICIDIN A COMPLRXED WITH POTASSIUM THIOCYANATE
SOLUTION STRUCTURE OF THE GRAMICIDIN A
SOLUTION STRUCTURE OF GRAMICIDIN A IN SODIUM DODECYL SULFATE MICELLES
SOLUTION STRUCTURE OF A LINKED SHORTENED GRAMICIDIN A IN BENZENE/ACETONE 10:1
SOLID STATE NMR STRUCTURE OF GRAMICIDIN A IN HYDRATED DMPC BILAYERS,
SOLUTION STRUCTURE OF GRAMICIDIN A IN METHANOL IN THE PRESENCE OF CACL
SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE MICELLES
SOLUTION STRUCTURE OF GRAMICIDIN A IN DODECYL PHOSPHOCHOLINE MICELLES IN THE PRESENCE OF EXCESS NA+
SOLUTION STRUCTURE OF GRAMICIDIN A (V1F) IN SODIUM DODECYL SULFATE MICELLES
SOLUTION STRUCTURE OF GRAMICIDIN B IN SODIUM DODECYL SULFATE MICELLES
SOLUTION STRUCTURE OF GRAMICIDIN C IN SODIUM DODECYL SULFATE MICELLES
SOLUTION STRUCTURE OF F1-GRAMICIDIN C IN SODIUM DODECYL SULFATE MICELLES
SOLUTION STRUCTURE OF A LINKED UNSYMMETRIC GRAMICIDIN A IN A MEMBRANE-ISOELECTRICAL SOLVENTS MIXTURE, IN THE PRESENCE OF CSCL
CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL
CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH KI IN METHANOL
CRYSTAL STRUCTURE OF GRAMICIDIN D COMPLEX WITH NAI
CRYSTAL STRUCTURE OF GRAMICIDIN D IN N-PROPANOL
CRYSTAL STRUCTURE OF GRAMICIDIN D IN METHANOL
CRYSTAL STRUCTURE OF GRAMICIDIN D IN ETHANOL
RCSB
Y
RCSB
2002-12-17
REL
MUTATION TRP15 TO GLY
1393
BREVIBACILLUS BREVIS
sample
GRAMICIDIN IS A HETEROGENEOUS MIXTURE OF SEVERAL COMPOUNDS
INCLUDING GRAMICIDIN A, B AND C WHICH ARE OBTAINED FROM
BACILLUS BREVIS AND CALLED COLLECTIVELY GRAMICIDIN D
HERE, GRAMICIDIN A IS REPRESENTED BY THE SEQUENCE (SEQRES)
Antibiotic
GRAMICIDIN A IS A HEXADECAMERIC HELICAL PEPTIDE
WITH ALTERNATING D,L CHARACTERISTICS.
THE N-TERM IS FORMYLATED (RESIDUE 0).
THE C-TERM IS CAPPED WITH ETHANOLAMINE (RESIDUE 16).
Mutant GRAMICIDIN A
Polypeptide
A 40MSEC MIXING TIME WAS USED IN THE NOESY EXPERIMENT FROM WHICH DISTANCE CONSTRAINTS WERE OBTAINED.
1
2D NOESY
6.5
AMBIENT
328
K
THE STRUCTURE WAS MODELED USING 530 DISTANCE CONSTRAINTS AND 13 HYDROGEN BOND CONSTRAINTS PER MONOMER, INCLUDING CONSTRAINTS BETWEEN THE MONOMERS. THE C2 SYMMETRY CONSTRAINT DOUBLES THIS NUMBER OF CONSTRAINTS FOR THE DIMER. 100 STRUCTURES WERE GENERATED USING DSPACE, OF WHICH THE 10 WITH THE FEWEST VIOLATIONS FROM THE DISTANCE CONSTRAINTS WERE CHOSEN FOR THE AVERAGE STRUCTURE. THIS AVERAGE STRUCTURE WAS FURTHER REFINED BY CONSTRAINED MINIMIZATION WITH DISCOVER USING THE ALL-ATOM AMBER FORCE FIELD AND A DIELECTRIC CONSTANT OF 2.0 TO EMULATE THAT OF THE MICELLE INTERIOR.
DISTANCE GEOMETRY, SIMULATED ANNEALING, RELAXATION MATRIX CALCULATION, MINIMIZATION
minimized average structure
5MM G15-GRAMICIDIN A, 250MM DEUTERATED SODIUM DODECYL SULFATE, 80% 100MM PHOSPHATE BUFFER PH 6.5, 10% D2O, 10% DEUTERATED TFE
BIOSYM/MSI
refinement
DISCOVER 97.2
structure solution
VNMR 3.2
structure solution
FELIX 95.0
structure solution
DSPACE 4.0
500
Varian
VXRS
FVA
1
n
1
FVA
1
A
GLY
2
n
2
GLY
2
A
ALA
3
n
3
ALA
3
A
DLE
4
n
4
DLE
4
A
ALA
5
n
5
ALA
5
A
DVA
6
n
6
DVA
6
A
VAL
7
n
7
VAL
7
A
DVA
8
n
8
DVA
8
A
TRP
9
n
9
TRP
9
A
DLE
10
n
10
DLE
10
A
TRP
11
n
11
TRP
11
A
DLE
12
n
12
DLE
12
A
TRP
13
n
13
TRP
13
A
DLE
14
n
14
DLE
14
A
GLY
15
n
15
GLY
15
A
ETA
16
n
16
ETA
16
A
FVA
1
n
1
FVA
1
B
GLY
2
n
2
GLY
2
B
ALA
3
n
3
ALA
3
B
DLE
4
n
4
DLE
4
B
ALA
5
n
5
ALA
5
B
DVA
6
n
6
DVA
6
B
VAL
7
n
7
VAL
7
B
DVA
8
n
8
DVA
8
B
TRP
9
n
9
TRP
9
B
DLE
10
n
10
DLE
10
B
TRP
11
n
11
TRP
11
B
DLE
12
n
12
DLE
12
B
TRP
13
n
13
TRP
13
B
DLE
14
n
14
DLE
14
B
GLY
15
n
15
GLY
15
B
ETA
16
n
16
ETA
16
B
author_and_software_defined_assembly
PISA
2
dimeric
780
-3.0
2650
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
ALA
3
A
N
ALA
3
B
O
ALA
3
B
O
ALA
3
minimized average
G15-Gramicidin A in Sodium Dodecyl Sulfate Micelles (NMR)
1
N
N
1
N
N
covale
1.342
both
A
FVA
1
A
C
FVA
1
1_555
A
GLY
2
A
N
GLY
2
1_555
covale
1.337
both
A
ALA
3
A
C
ALA
3
1_555
A
DLE
4
A
N
DLE
4
1_555
covale
1.340
both
A
DLE
4
A
C
DLE
4
1_555
A
ALA
5
A
N
ALA
5
1_555
covale
1.341
both
A
ALA
5
A
C
ALA
5
1_555
A
DVA
6
A
N
DVA
6
1_555
covale
1.342
both
A
DVA
6
A
C
DVA
6
1_555
A
VAL
7
A
N
VAL
7
1_555
covale
1.337
both
A
VAL
7
A
C
VAL
7
1_555
A
DVA
8
A
N
DVA
8
1_555
covale
1.339
both
A
DVA
8
A
C
DVA
8
1_555
A
TRP
9
A
N
TRP
9
1_555
covale
1.343
both
A
TRP
9
A
C
TRP
9
1_555
A
DLE
10
A
N
DLE
10
1_555
covale
1.340
both
A
DLE
10
A
C
DLE
10
1_555
A
TRP
11
A
N
TRP
11
1_555
covale
1.339
both
A
TRP
11
A
C
TRP
11
1_555
A
DLE
12
A
N
DLE
12
1_555
covale
1.341
both
A
DLE
12
A
C
DLE
12
1_555
A
TRP
13
A
N
TRP
13
1_555
covale
1.342
both
A
TRP
13
A
C
TRP
13
1_555
A
DLE
14
A
N
DLE
14
1_555
covale
1.339
both
A
DLE
14
A
C
DLE
14
1_555
A
GLY
15
A
N
GLY
15
1_555
covale
1.340
both
A
GLY
15
A
C
GLY
15
1_555
A
ETA
16
A
N
ETA
16
1_555
covale
1.342
both
B
FVA
1
B
C
FVA
1
1_555
B
GLY
2
B
N
GLY
2
1_555
covale
1.337
both
B
ALA
3
B
C
ALA
3
1_555
B
DLE
4
B
N
DLE
4
1_555
covale
1.339
both
B
DLE
4
B
C
DLE
4
1_555
B
ALA
5
B
N
ALA
5
1_555
covale
1.341
both
B
ALA
5
B
C
ALA
5
1_555
B
DVA
6
B
N
DVA
6
1_555
covale
1.342
both
B
DVA
6
B
C
DVA
6
1_555
B
VAL
7
B
N
VAL
7
1_555
covale
1.337
both
B
VAL
7
B
C
VAL
7
1_555
B
DVA
8
B
N
DVA
8
1_555
covale
1.339
both
B
DVA
8
B
C
DVA
8
1_555
B
TRP
9
B
N
TRP
9
1_555
covale
1.343
both
B
TRP
9
B
C
TRP
9
1_555
B
DLE
10
B
N
DLE
10
1_555
covale
1.340
both
B
DLE
10
B
C
DLE
10
1_555
B
TRP
11
B
N
TRP
11
1_555
covale
1.338
both
B
TRP
11
B
C
TRP
11
1_555
B
DLE
12
B
N
DLE
12
1_555
covale
1.340
both
B
DLE
12
B
C
DLE
12
1_555
B
TRP
13
B
N
TRP
13
1_555
covale
1.342
both
B
TRP
13
B
C
TRP
13
1_555
B
DLE
14
B
N
DLE
14
1_555
covale
1.341
both
B
DLE
14
B
C
DLE
14
1_555
B
GLY
15
B
N
GLY
15
1_555
covale
1.340
both
B
GLY
15
B
C
GLY
15
1_555
B
ETA
16
B
N
ETA
16
1_555
ANTIBIOTIC
ANTIBIOTIC, GRAMICIDIN, ANTIFUNGAL, ANTIBACTERIAL, SDS MICELLES, MEMBRANE ION CHANNEL, LINEAR GRAMICIDIN
NOR00243
NOR
1
NOR00243
1
16
1NG8
1
16
NOR00243
A
1
1
16
1
16
1NG8
1
16
NOR00243
B
1
1
16
1
TRP
engineered mutation
GLY
15
1NG8
A
NOR00243
NOR
15
15
2
TRP
engineered mutation
GLY
15
1NG8
B
NOR00243
NOR
15
15
2
anti-parallel
A
GLY
2
A
GLY
2
A
GLY
15
A
GLY
15
B
GLY
2
B
GLY
2
B
GLY
15
B
GLY
15
BINDING SITE FOR CHAIN A OF GRAMICIDIN A
Software
3
BINDING SITE FOR CHAIN B OF GRAMICIDIN A
Software
3
B
ALA
3
B
ALA
3
3
1_555
B
DLE
4
B
DLE
4
3
1_555
B
ALA
5
B
ALA
5
3
1_555
A
ALA
3
A
ALA
3
3
1_555
A
DLE
4
A
DLE
4
3
1_555
A
ALA
5
A
ALA
5
3
1_555
1
P 1