1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Gordon, L.M.
Mobley, P.W.
Lee, W.
Eskandari, S.
Kaznessis, Y.N.
Sherman, M.A.
Waring, A.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
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 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
H2 N
16.023
AMINO GROUP
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Protein Sci.
PRCIEI
0795
0961-8368
13
1012
1030
10.1110/ps.03407704
15044732
Conformational mapping of the N-terminal peptide of HIV-1 gp41 in lipid detergent and aqueous environments using 13C-enhanced Fourier transform infrared spectroscopy.
2004
NE
BIOCHIM.BIOPHYS.ACTA
BBACAQ
0113
0006-3002
1559
96
120
10.1016/S0005-2736(01)00443-6
CONFORMATIONAL MAPPING OF THE N-TERMINAL PEPTIDE OF HIV-1 GP41 IN MEMBRANE ENVIRONMENTS USING 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY
2002
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
1
SINGLE WAVELENGTH
M
1
1.0
C-terminus has been amidated
2123.481
Envelope polyprotein GP160
residues 519-541
1
syn
polymer
N-terminal fusion peptide of HIV-1 GP41
no
yes
AVGIGALFLGFLGAAGSTMGARS(NH2)
AVGIGALFLGFLGAAGSTMGARSX
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
repository
Initial release
Version format compliance
Version format compliance
1
0
2003-05-20
1
1
2008-04-29
1
2
2011-07-13
CONFORMATIONAL MAPPING OF THE N-TERMINAL PEPTIDE OF HIV-1 GP41 IN MEMBRANE ENVIRONMENTS USING 13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY
REMARK: THIS STRUCTURE WAS DETERMINED BY MEANS OF
13C-ENHANCED FOURIER TRANSFORM INFRARED SPECTROSCOPY
(FTIR). DATA SET CONSISTS OF 19 CONFORMERS DERIVED
FROM MOLECULAR DYNAMICS IN A MODELED SDS MICELLE
SURROUNDED BY WATER WITH PEPTIDE BACKBONE CONSTRAINTS
FROM FTIR.
EXPERIMENTAL DETAILS
EXPERIMENT TYPE : INFRARED SPECTROSCOPY
TEMPERATURE (KELVIN) : 298
PH : 7.4
IONIC STRENGTH : 0.271
PRESSURE : AMBIENT
SAMPLE CONTENTS : THIS STRUCTURE WAS DETERMINED
USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF
SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C
CARBONYL LABELS INCLUDED RESIDUES 519,521,523,524,525,526,527,
528,529,530,531,532,533,534,538,539.
EXPERIMENTS CONDUCTED : 13C-ISOTOPE ENHANCED FTIR
SPECTROMETER FIELD STRENGTH : NULL
SPECTROMETER MODEL : RESEARCH SERIES
SPECTROMETER MANUFACTURER : MATTSON FTIR
STRUCTURE DETERMINATION.
SOFTWARE USED : WINFIRST FTIR CURVE FITTING
SOFTWARE
METHOD USED : MOLECULAR DYNAMICS
CONFORMERS, NUMBER CALCULATED : 20
CONFORMERS, NUMBER SUBMITTED : 19
CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH ACCEPTABLE
COVALENT GEOMETRY
BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1
REMARK: THE COORDINATES IN THIS ENTRY WERE GENERATED FROM 13-C
INDUCED SPECTRAL SHIFTS WHICH GIVE RESIDUE-SPECIFIC SECONDARY
STRUCTURE INFORMATION. PEPTIDE CONCENTRATION WAS 47
MICROMOLAR. PEPTIDE/SDS RATIO WAS 1/200. FTIR SPECTRA WERE
AVERAGED OVER 256 SCANS AT A GAIN OF 4 AND A RESOLUTION OF 2
CM-1
RCSB
Y
RCSB
2003-04-25
REL
The sequence of this peptide occurs naturally in human immunodeficiency virus glycoprotein 41.
sample
The coordinates in this entry were generated from 13-C induced spectral shifts which give residue-specific secondary structure information. Peptide concentration was 47 micromolar. Peptide/SDS ratio was 1/200. FTIR spectra were averaged over 256 scans at a gain of 4 and a resolution of 2 cm-1
structures with acceptable covalent geometry
20
19
13C-isotope enhanced FTIR
0.271
7.4
ambient
298
The system of more than 16,000 atoms (peptide, SDS micelle, water, sodium counterions) was simulated for 2.5 nanoseconds at a constant pressure P=1 atm and constant temperature T=303.15 K.
molecular dynamics
1
closest to the average
THIS STRUCTURE WAS DETERMINED USING 13-C ISOTOPE ENHANCED FTIR SPECTROSCOPY ON A FAMILY OF SELECTIVELY LABELED CHEMICALLY SYNTHESIZED PEPTIDES. 13-C CARBONYL LABELS INCLUDED RESIDUES 519,521,523,524,525,526,527,528,529,530,531,532,533,534,538,539.
94 mM SDS (sodium dodecyl sulfate) in deuterated PBS (phosphate buffered saline), where PBS is 120 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4
Kauppine et al.
data analysis
Winfirst
FTIR curve fitting software
Brooks et al.
refinement
CHARMM
c28b2
Mattson FTIR
Research Series
ALA
1
n
1
ALA
1
A
VAL
2
n
2
VAL
2
A
GLY
3
n
3
GLY
3
A
ILE
4
n
4
ILE
4
A
GLY
5
n
5
GLY
5
A
ALA
6
n
6
ALA
6
A
LEU
7
n
7
LEU
7
A
PHE
8
n
8
PHE
8
A
LEU
9
n
9
LEU
9
A
GLY
10
n
10
GLY
10
A
PHE
11
n
11
PHE
11
A
LEU
12
n
12
LEU
12
A
GLY
13
n
13
GLY
13
A
ALA
14
n
14
ALA
14
A
ALA
15
n
15
ALA
15
A
GLY
16
n
16
GLY
16
A
SER
17
n
17
SER
17
A
THR
18
n
18
THR
18
A
MET
19
n
19
MET
19
A
GLY
20
n
20
GLY
20
A
ALA
21
n
21
ALA
21
A
ARG
22
n
22
ARG
22
A
SER
23
n
23
SER
23
A
NH2
24
n
24
NH2
24
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
10
A
A
ALA
GLY
15
16
148.84
1
A
PHE
11
0.070
SIDE CHAIN
2
A
ARG
22
0.179
SIDE CHAIN
5
A
PHE
11
0.081
SIDE CHAIN
6
A
ARG
22
0.080
SIDE CHAIN
9
A
PHE
8
0.086
SIDE CHAIN
9
A
ARG
22
0.119
SIDE CHAIN
10
A
PHE
11
0.112
SIDE CHAIN
13
A
PHE
11
0.093
SIDE CHAIN
14
A
PHE
8
0.070
SIDE CHAIN
14
A
ARG
22
0.074
SIDE CHAIN
16
A
ARG
22
0.115
SIDE CHAIN
19
A
ARG
22
0.082
SIDE CHAIN
1
-7.37
0.70
120.80
113.43
A
A
A
CB
CG
CD1
PHE
PHE
PHE
8
8
8
N
1
-15.32
1.60
100.20
84.88
A
A
A
CG
SD
CE
MET
MET
MET
19
19
19
N
1
3.27
0.50
120.30
123.57
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
22
22
22
N
1
-3.49
0.50
120.30
116.81
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
22
22
22
N
2
7.04
0.50
120.30
127.34
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
22
22
22
N
2
-8.04
0.50
120.30
112.26
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
22
22
22
N
3
-5.70
0.70
120.80
115.10
A
A
A
CB
CG
CD2
PHE
PHE
PHE
8
8
8
N
3
-6.47
0.70
120.80
114.33
A
A
A
CB
CG
CD2
PHE
PHE
PHE
11
11
11
N
3
5.13
0.70
120.80
125.93
A
A
A
CB
CG
CD1
PHE
PHE
PHE
11
11
11
N
3
-4.11
0.50
120.30
116.19
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
22
22
22
N
4
6.06
0.70
120.80
126.86
A
A
A
CB
CG
CD1
PHE
PHE
PHE
11
11
11
N
4
10.39
1.70
111.00
121.39
A
A
A
CB
CG
CD2
LEU
LEU
LEU
12
12
12
N
4
3.21
0.50
120.30
123.51
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
22
22
22
N
5
-5.27
0.70
120.80
115.53
A
A
A
CB
CG
CD1
PHE
PHE
PHE
11
11
11
N
5
4.69
0.50
120.30
124.99
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
22
22
22
N
6
5.03
0.50
120.30
125.33
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
22
22
22
N
6
-5.79
0.50
120.30
114.51
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
22
22
22
N
7
-3.05
0.50
120.30
117.25
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
22
22
22
N
8
-8.35
0.70
120.80
112.45
A
A
A
CB
CG
CD2
PHE
PHE
PHE
11
11
11
N
8
4.25
0.70
120.80
125.05
A
A
A
CB
CG
CD1
PHE
PHE
PHE
11
11
11
N
9
-7.44
0.70
120.80
113.36
A
A
A
CB
CG
CD2
PHE
PHE
PHE
11
11
11
N
9
4.87
0.70
120.80
125.67
A
A
A
CB
CG
CD1
PHE
PHE
PHE
11
11
11
N
10
-5.17
0.70
120.80
115.63
A
A
A
CB
CG
CD2
PHE
PHE
PHE
11
11
11
N
11
-4.32
0.70
120.80
116.48
A
A
A
CB
CG
CD1
PHE
PHE
PHE
11
11
11
N
11
3.87
0.50
120.30
124.17
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
22
22
22
N
11
-8.06
0.50
120.30
112.24
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
22
22
22
N
12
4.58
0.70
120.80
125.38
A
A
A
CB
CG
CD2
PHE
PHE
PHE
11
11
11
N
12
4.48
0.50
120.30
124.78
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
22
22
22
N
12
-8.13
0.50
120.30
112.17
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
22
22
22
N
13
7.06
0.50
120.30
127.36
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
22
22
22
N
13
11.17
1.50
110.50
121.67
A
A
A
N
CA
CB
SER
SER
SER
23
23
23
N
14
-9.55
1.40
110.10
100.55
A
A
A
N
CA
CB
ALA
ALA
ALA
6
6
6
N
14
-15.99
2.50
113.10
97.11
A
A
A
N
CA
C
GLY
GLY
GLY
20
20
20
N
14
-3.47
0.50
120.30
116.83
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
22
22
22
N
15
8.67
1.40
110.10
118.77
A
A
A
N
CA
CB
ALA
ALA
ALA
15
15
15
N
15
6.71
0.50
120.30
127.01
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
22
22
22
N
16
-4.77
0.50
120.30
115.53
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
22
22
22
N
17
3.93
0.50
120.30
124.23
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
22
22
22
N
17
-3.86
0.50
120.30
116.44
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
22
22
22
N
18
3.33
0.50
120.30
123.63
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
22
22
22
N
19
-7.60
0.70
120.80
113.20
A
A
A
CB
CG
CD2
PHE
PHE
PHE
11
11
11
N
19
3.18
0.50
120.30
123.48
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
22
22
22
N
1
A
A
CG
CD1
PHE
PHE
11
11
0.091
0.015
1.383
1.474
N
3
A
A
CA
CB
SER
SER
23
23
0.093
0.015
1.525
1.618
N
4
A
A
CA
CB
SER
SER
17
17
0.095
0.015
1.525
1.620
N
5
A
A
CA
CB
SER
SER
17
17
0.113
0.015
1.525
1.638
N
12
A
A
CZ
CE2
PHE
PHE
8
8
0.122
0.019
1.369
1.491
N
16
A
A
CG
CD2
PHE
PHE
11
11
0.100
0.015
1.383
1.483
N
18
A
A
CG
CD2
PHE
PHE
8
8
0.095
0.015
1.383
1.478
N
1
A
ALA
15
-91.29
-89.98
2
A
ALA
14
-73.60
-70.77
2
A
SER
17
-145.37
-141.56
2
A
MET
19
-91.25
-100.74
3
A
ARG
22
-65.84
-90.46
5
A
ARG
22
-97.21
-82.71
6
A
MET
19
-95.59
-64.87
6
A
ARG
22
-78.04
-79.87
7
A
LEU
7
-81.09
-71.32
7
A
MET
19
-103.44
-95.36
7
A
ARG
22
-83.95
-96.63
8
A
LEU
12
-57.90
-81.92
8
A
ALA
15
-62.66
-88.43
8
A
ARG
22
-94.70
-137.81
9
A
LEU
7
-73.33
-73.50
9
A
ARG
22
-81.08
-106.06
10
A
LEU
7
-61.71
-70.00
10
A
ARG
22
-93.28
-70.37
11
A
LEU
7
-63.86
-82.49
11
A
ALA
14
-53.37
-72.21
11
A
ARG
22
-100.09
-69.05
12
A
ALA
15
-65.27
-71.38
12
A
MET
19
-83.30
-74.98
15
A
MET
19
-98.21
-84.46
16
A
ARG
22
-84.12
-73.65
17
A
LEU
7
-70.35
-70.70
18
A
VAL
2
-104.46
-167.74
18
A
LEU
7
-77.53
-74.68
18
A
ARG
22
-79.58
-85.01
19
A
ALA
15
-60.57
-83.69
19
A
SER
17
-57.47
179.36
19
A
ARG
22
-100.92
-103.97
Envelope polyprotein GP160
Conformational Mapping of the N-terminal Peptide of HIV-1 GP41 in lipid detergent and aqueous environments using 13C-enhanced Fourier Transform Infrared Spectroscopy
1
N
N
A
GLY
3
A
GLY
3
HELX_P
A
PHE
8
A
PHE
8
1
1
6
covale
1.316
A
SER
23
A
C
SER
23
1_555
A
NH2
24
A
N
NH2
24
1_555
VIRAL PROTEIN
human immunodeficiency virus (HIV-1), viral fusion peptide, gp41, Viral protein
ENV_HV1BR
UNP
1
517
P03377
AVGIGALFLGFLGAAGSTMGARS
517
539
1P5A
1
23
P03377
A
1
1
23
BINDING SITE FOR RESIDUE NH2 A 24
Software
1
A
SER
23
A
SER
23
1
1_555