1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Cady, S.D.
Schmidt-Rohr, K.
Wang, J.
Soto, C.S.
DeGrado, W.F.
Hong, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
1
90.00
90.00
90.00
1.000
1.000
1.000
C10 H17 N
151.249
(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine
Amantadine
non-polymer
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
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 H13 N O2
131.173
y
LEUCINE
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
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
UK
Nature
NATUAS
0006
0028-0836
463
689
692
10.1038/nature08722
20130653
Structure of the amantadine binding site of influenza M2 proton channels in lipid bilayers
2010
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
385
1127
1141
10.1016/j.jmb.2008.11.022
19061899
Structure of amantadine-bound M2 transmembrane peptide of influenza A in lipid bilayers from magic-angle-spinning solid-state NMR: the role of Ser31 in amantadine binding.
2009
US
Biophys.J.
BIOJAU
0030
0006-3495
92
4335
4343
10.1529/biophysj.106.090183
17384070
Backbone structure of the amantadine-blocked trans-membrane domain M2 proton channel from Influenza A virus.
2007
10.2210/pdb2kqt/pdb
pdb_00002kqt
1
1
1.0
2730.295
M2 protein
residues 22-46
4
syn
polymer
151.249
(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine
1
syn
non-polymer
no
no
SSDPLVVAASIIGILHLILWILDRL
SSDPLVVAASIIGILHLILWILDRL
A,B,C,D
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
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_nmr_spectrometer
database_2
pdbx_database_status
repository
Initial release
Version format compliance
Other
Data collection
Database references
Other
Database references
Other
1
0
2010-02-09
1
1
2011-07-13
1
2
2011-10-26
1
3
2020-02-26
1
4
2023-06-14
_pdbx_database_status.status_code_cs
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
Magic-Angle-Spinning Solid-State NMR Structure of Influenza A M2 Transmembrane Domain
Structure of the Amantadine-Blocked Influenza A M2 Proton Channel Trans-membrane Domain by Solid-state NMR spectroscopy
Proton Channel M2 from Influenza A in complex with inhibitor rimantadine
The Crystal structure of Transmembrane domain of M2 protein and Amantadine complex
The closed state structure of M2 protein H+ channel by solid state NMR spectroscopy
High resolution Crystal structure of Transmembrane domain of M2 protein
THIS ENTRY 2KQT REFLECTS AN ALTERNATIVE MODELING OF THE
ORIGINAL STRUCTURAL DATA 2H95 and 2KAD
BMRB
Y
RCSB
2009-11-18
REL
REL
REL
REL
308
(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]decan-1-amine
Solid-phase synthesis
sample
8
structures with the least restraint violations
24
17
2D 13C-13C Spin Diffusion
2D 13C-13C Spin Diffusion
2D 13C-13C Spin Diffusion
2D 13C-15N HETCOR
2D 13C-15N HETCOR
2D 13C-15N HETCOR
1D 2H-13C REDOR, single 13C pulse
1D 2H-13C REDOR, single 13C pulse
1D 2H-13C REDOR, single 13C pulse
1D 2H-13C REDOR, single 13C pulse
1D 2H-13C REDOR, single 2H pulse
1D 2H-13C REDOR, single 2H pulse
1D 2H-13C REDOR, single 2H pulse
2H Static Quadrupolar Echo
2H Static Quadrupolar Echo
2H Static Quadrupolar Echo
5.8
mg/mL
[U-99% 13C; U-99% 15N] at S31, I32 and D44
21.6
mg/mL
10
mM
10
mM
1
mM
.1
mM
.42
mg/mL
[U-2H]
5.0
mg/mL
[U-99% 13C; U-99% 15N] at S31, I32 and D44
10.4
mg/mL
10
mM
10
mM
1
mM
0.1
mM
0.09
mg/mL
[U-2H]
5.2
mg/mL
[U-99% 13C; U-99% 15N] at L26, V27, A29 and G34
19.9
mg/mL
10
mM
10
mM
1
mM
.1
mM
0.38
mg/mL
[U-2H]
7
mg/mL
[U-99% 13C; U-99% 15N] at L26, V27, A29 and G34
27
mg/mL
10
mM
10
mM
1
mM
.1
mM
2.0
mg/mL
[U-2H]
7
mg/mL
[U-99% 13C; U-99% 15N] at L26, V27, A29 and G34
27
mg/mL
10
mM
10
mM
1
mM
.1
mM
0.5
mg/mL
[U-2H]
7.5
ambient
243
K
The temperature was initially set to 1,000,000K and decreased by 10% every 100 steps until a temperature of 25 K was reached. The constants (CI-CIV) were obtained through a trial-and-error process. Some side chain rotamers were changed to maximize agreement with the radial distances., An ensemble of models was obtained by selecting the top scoring model after one round of Monte Carlo/Simulated Annealing minimization and refining again with the inverse kinematics algorithm. The distance potential constant CIII was set to 50 kcal/mol-radians^2. Since the radial distance provided excellent restraints between the drug and M2, we were able to position the amantidine molecule near with S31 without the need for further minimization.
THE POSITION OF THE AMANTADINE LIGAND (PDB CODE 308) IS IDENTICAL IN ALL OF THE MINIMIZED STRUCTURE SINCE IT IS THE AVERAGE LIGAND POSITION RELATIVE TO THE BACKBONE. WE HAVE MEASURED A 13C-2H DIPOLAR COUPLING FROM SEVERAL PEPTIDE BACKBONE AND SIDECHAIN CARBONS TO THE DEUTERONS ON THE 308 LIGAND. WE SIMULATED THE THE RADIUS OF THE M2 CHANNEL PORE FOR THE SITES WHERE WE OBSERVED 13C-2H DIPOLAR COUPLING, AND FOUND PORE RADII FOR THESE SITES THAT CORRESPONDED WITH THE MEASURED 13C-2H DIPOLAR COUPLING AT THAT SITE. THUS, IN THE FINAL STRUCTURE MINIMIZATION, WE USED THE PORE RADII AS A CONSTRAINT RATHER THAN PEPTIDE-DRUG DISTANCES SINCE THE LIGAND IS ROTATING IN THE CHANNEL.
simulated annealing, Monte Carlo
1
fewest violations
5.8 mg [U-99% 13C; U-99% 15N] at S31, I32 and D44 M2-TM, 21.6 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, .42 mg [U-2H] d15-1-aminoadamantane*HCl, 10mM pH 7.5 phosphate buffer, 50% hydration
10mM pH 7.5 phosphate buffer, 50% hydration
5.0 mg [U-99% 13C; U-99% 15N] at S31, I32 and D44 M2-TM, 10.4 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 0.09 mg [U-2H] d15-1-aminoadamantane*HCl, 10mM pH 7.5 phosphate buffer, 50% hydration
10mM pH 7.5 phosphate buffer, 50% hydration
5.2 mg [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 M2-TM, 19.9 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 0.38 mg [U-2H] d15-1-aminoadamantane*HCl, 10mM pH 7.5 phosphate buffer, 50% hydration
10mM pH 7.5 phosphate buffer, 50% hydration
7 mg [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 M2-TM, 27 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO4, 1 mM EDTA, 0.1 mM NaN3, 2.0 mg [U-2H] d15-1-aminoadamantane*HCl, 10mM pH 7.5 phosphate buffer, 50% hydration
10mM pH 7.5 phosphate buffer, 50% hydration
7 mg [U-99% 13C; U-99% 15N] at L26, V27, A29 and G34 M2-TM, 27 mg DMPC, 10 mM NaH2PO4, 10 mM Na2HPO, 1 mM EDTA, 0.1 mM NaN3, 0.5 mg [U-2H] d15-1-aminoadamantane*HCl, 10mM pH 7.5 phosphate buffer, 50% hydration
10mM pH 7.5 phosphate buffer, 50% hydration
Bruker Biospin
collection
TopSpin
1.3
Bruker Biospin
chemical shift assignment
TopSpin
1.3
Bruker Biospin
processing
TopSpin
1.3
Bruker Biospin
data analysis
TopSpin
1.3
Bruker Biospin
peak picking
TopSpin
1.3
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR_NIH, IN-HOUSE METHOD
Bruker Biospin
collection
XwinNMR
Bruker Biospin
chemical shift assignment
XwinNMR
400
Bruker
AVANCE
Bruker Avance
600
Bruker
AVANCE
Bruker Avance
308
1
2
308
308
1
C
SER
22
n
1
SER
22
A
SER
23
n
2
SER
23
A
ASP
24
n
3
ASP
24
A
PRO
25
n
4
PRO
25
A
LEU
26
n
5
LEU
26
A
VAL
27
n
6
VAL
27
A
VAL
28
n
7
VAL
28
A
ALA
29
n
8
ALA
29
A
ALA
30
n
9
ALA
30
A
SER
31
n
10
SER
31
A
ILE
32
n
11
ILE
32
A
ILE
33
n
12
ILE
33
A
GLY
34
n
13
GLY
34
A
ILE
35
n
14
ILE
35
A
LEU
36
n
15
LEU
36
A
HIS
37
n
16
HIS
37
A
LEU
38
n
17
LEU
38
A
ILE
39
n
18
ILE
39
A
LEU
40
n
19
LEU
40
A
TRP
41
n
20
TRP
41
A
ILE
42
n
21
ILE
42
A
LEU
43
n
22
LEU
43
A
ASP
44
n
23
ASP
44
A
ARG
45
n
24
ARG
45
A
LEU
46
n
25
LEU
46
A
SER
22
n
1
SER
22
B
SER
23
n
2
SER
23
B
ASP
24
n
3
ASP
24
B
PRO
25
n
4
PRO
25
B
LEU
26
n
5
LEU
26
B
VAL
27
n
6
VAL
27
B
VAL
28
n
7
VAL
28
B
ALA
29
n
8
ALA
29
B
ALA
30
n
9
ALA
30
B
SER
31
n
10
SER
31
B
ILE
32
n
11
ILE
32
B
ILE
33
n
12
ILE
33
B
GLY
34
n
13
GLY
34
B
ILE
35
n
14
ILE
35
B
LEU
36
n
15
LEU
36
B
HIS
37
n
16
HIS
37
B
LEU
38
n
17
LEU
38
B
ILE
39
n
18
ILE
39
B
LEU
40
n
19
LEU
40
B
TRP
41
n
20
TRP
41
B
ILE
42
n
21
ILE
42
B
LEU
43
n
22
LEU
43
B
ASP
44
n
23
ASP
44
B
ARG
45
n
24
ARG
45
B
LEU
46
n
25
LEU
46
B
SER
22
n
1
SER
22
C
SER
23
n
2
SER
23
C
ASP
24
n
3
ASP
24
C
PRO
25
n
4
PRO
25
C
LEU
26
n
5
LEU
26
C
VAL
27
n
6
VAL
27
C
VAL
28
n
7
VAL
28
C
ALA
29
n
8
ALA
29
C
ALA
30
n
9
ALA
30
C
SER
31
n
10
SER
31
C
ILE
32
n
11
ILE
32
C
ILE
33
n
12
ILE
33
C
GLY
34
n
13
GLY
34
C
ILE
35
n
14
ILE
35
C
LEU
36
n
15
LEU
36
C
HIS
37
n
16
HIS
37
C
LEU
38
n
17
LEU
38
C
ILE
39
n
18
ILE
39
C
LEU
40
n
19
LEU
40
C
TRP
41
n
20
TRP
41
C
ILE
42
n
21
ILE
42
C
LEU
43
n
22
LEU
43
C
ASP
44
n
23
ASP
44
C
ARG
45
n
24
ARG
45
C
LEU
46
n
25
LEU
46
C
SER
22
n
1
SER
22
D
SER
23
n
2
SER
23
D
ASP
24
n
3
ASP
24
D
PRO
25
n
4
PRO
25
D
LEU
26
n
5
LEU
26
D
VAL
27
n
6
VAL
27
D
VAL
28
n
7
VAL
28
D
ALA
29
n
8
ALA
29
D
ALA
30
n
9
ALA
30
D
SER
31
n
10
SER
31
D
ILE
32
n
11
ILE
32
D
ILE
33
n
12
ILE
33
D
GLY
34
n
13
GLY
34
D
ILE
35
n
14
ILE
35
D
LEU
36
n
15
LEU
36
D
HIS
37
n
16
HIS
37
D
LEU
38
n
17
LEU
38
D
ILE
39
n
18
ILE
39
D
LEU
40
n
19
LEU
40
D
TRP
41
n
20
TRP
41
D
ILE
42
n
21
ILE
42
D
LEU
43
n
22
LEU
43
D
ASP
44
n
23
ASP
44
D
ARG
45
n
24
ARG
45
D
LEU
46
n
25
LEU
46
D
author_defined_assembly
4
tetrameric
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
GLY
34
-15.25
1
B
GLY
34
-15.25
1
C
GLY
34
-15.25
1
D
GLY
34
-15.25
2
A
GLY
34
-15.32
2
B
GLY
34
-15.32
2
C
GLY
34
-15.32
2
D
GLY
34
-15.32
3
A
GLY
34
-15.22
3
B
GLY
34
-15.22
3
C
GLY
34
-15.22
3
D
GLY
34
-15.22
4
A
GLY
34
-15.25
4
B
GLY
34
-15.25
4
C
GLY
34
-15.25
4
D
GLY
34
-15.25
5
A
GLY
34
-15.24
5
B
GLY
34
-15.24
5
C
GLY
34
-15.24
5
D
GLY
34
-15.24
6
A
GLY
34
-15.24
6
B
GLY
34
-15.24
6
C
GLY
34
-15.24
6
D
GLY
34
-15.24
7
A
GLY
34
-15.23
7
B
GLY
34
-15.23
7
C
GLY
34
-15.23
7
D
GLY
34
-15.23
8
A
GLY
34
-15.25
8
B
GLY
34
-15.25
8
C
GLY
34
-15.25
8
D
GLY
34
-15.25
9
A
GLY
34
-15.27
9
B
GLY
34
-15.27
9
C
GLY
34
-15.27
9
D
GLY
34
-15.27
10
A
GLY
34
-15.23
10
B
GLY
34
-15.23
10
C
GLY
34
-15.23
10
D
GLY
34
-15.23
11
A
GLY
34
-15.27
11
B
GLY
34
-15.27
11
C
GLY
34
-15.27
11
D
GLY
34
-15.27
12
A
GLY
34
-15.28
12
B
GLY
34
-15.28
12
C
GLY
34
-15.28
12
D
GLY
34
-15.28
13
A
GLY
34
-15.24
13
B
GLY
34
-15.24
13
C
GLY
34
-15.24
13
D
GLY
34
-15.24
14
A
GLY
34
-15.28
14
B
GLY
34
-15.28
14
C
GLY
34
-15.28
14
D
GLY
34
-15.28
15
A
GLY
34
-15.30
15
B
GLY
34
-15.30
15
C
GLY
34
-15.30
15
D
GLY
34
-15.30
16
A
GLY
34
-15.31
16
B
GLY
34
-15.31
16
C
GLY
34
-15.31
16
D
GLY
34
-15.31
17
A
GLY
34
-15.25
17
B
GLY
34
-15.25
17
C
GLY
34
-15.25
17
D
GLY
34
-15.25
1
A
SER
23
-123.82
-167.72
1
B
SER
23
-123.82
-167.72
1
C
SER
23
-123.82
-167.72
1
D
SER
23
-123.82
-167.72
2
A
SER
23
-122.24
-167.89
2
B
SER
23
-122.24
-167.89
2
C
SER
23
-122.24
-167.89
2
D
SER
23
-122.24
-167.89
3
A
SER
23
-121.93
-166.76
3
B
SER
23
-121.93
-166.76
3
C
SER
23
-121.93
-166.76
3
D
SER
23
-121.93
-166.76
4
A
SER
23
-121.59
-167.19
4
B
SER
23
-121.59
-167.19
4
C
SER
23
-121.59
-167.19
4
D
SER
23
-121.59
-167.19
5
A
SER
23
-121.03
-166.86
5
B
SER
23
-121.03
-166.86
5
C
SER
23
-121.03
-166.86
5
D
SER
23
-121.03
-166.86
6
A
SER
23
-121.08
-167.07
6
B
SER
23
-121.08
-167.07
6
C
SER
23
-121.08
-167.07
6
D
SER
23
-121.08
-167.07
7
A
SER
23
-121.66
-167.36
7
B
SER
23
-121.66
-167.36
7
C
SER
23
-121.66
-167.36
7
D
SER
23
-121.66
-167.36
8
A
SER
23
-122.81
-167.85
8
B
SER
23
-122.81
-167.85
8
C
SER
23
-122.81
-167.85
8
D
SER
23
-122.81
-167.85
9
A
SER
23
-122.37
-167.42
9
B
SER
23
-122.37
-167.42
9
C
SER
23
-122.37
-167.42
9
D
SER
23
-122.37
-167.42
10
A
SER
23
-123.11
-166.78
10
B
SER
23
-123.11
-166.78
10
C
SER
23
-123.11
-166.78
10
D
SER
23
-123.11
-166.78
11
A
SER
23
-122.89
-166.50
11
B
SER
23
-122.89
-166.50
11
C
SER
23
-122.89
-166.50
11
D
SER
23
-122.89
-166.50
12
A
SER
23
-124.50
-165.70
12
B
SER
23
-124.50
-165.70
12
C
SER
23
-124.50
-165.70
12
D
SER
23
-124.50
-165.70
13
A
SER
23
-124.12
-165.71
13
B
SER
23
-124.12
-165.71
13
C
SER
23
-124.12
-165.71
13
D
SER
23
-124.12
-165.71
14
A
SER
23
-124.33
-165.77
14
B
SER
23
-124.33
-165.77
14
C
SER
23
-124.33
-165.77
14
D
SER
23
-124.33
-165.77
15
A
SER
23
-123.57
-166.13
15
B
SER
23
-123.57
-166.13
15
C
SER
23
-123.57
-166.13
15
D
SER
23
-123.57
-166.13
16
A
SER
23
-123.17
-166.53
16
B
SER
23
-123.17
-166.53
16
C
SER
23
-123.17
-166.53
16
D
SER
23
-123.17
-166.53
17
A
SER
23
-122.63
-166.47
17
B
SER
23
-122.63
-166.47
17
C
SER
23
-122.63
-166.47
17
D
SER
23
-122.63
-166.47
fewest violations, model 1
Solid-state NMR structure of the M2 transmembrane peptide of the influenza A virus in DMPC lipid bilayers bound to deuterated amantadine
1
N
N
1
N
N
1
N
N
1
N
N
2
N
N
A
ASP
24
A
ASP
3
HELX_P
A
LEU
46
A
LEU
25
1
1
23
B
ASP
24
B
ASP
3
HELX_P
B
LEU
46
B
LEU
25
1
2
23
C
ASP
24
C
ASP
3
HELX_P
C
LEU
46
C
LEU
25
1
3
23
D
ASP
24
D
ASP
3
HELX_P
D
LEU
46
D
LEU
25
1
4
23
TRANSPORT PROTEIN
influenza, transmembrane, amantadine, REDOR, TRANSPORT PROTEIN
Q9YP62_9INFA
UNP
1
22
Q9YP62
SSDPLVVAASIIGILHLILWILDRL
22
46
2KQT
22
46
Q9YP62
A
1
1
25
22
46
2KQT
22
46
Q9YP62
B
1
1
25
22
46
2KQT
22
46
Q9YP62
C
1
1
25
22
46
2KQT
22
46
Q9YP62
D
1
1
25
1
P 1