1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
Reardon, P.N.
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
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
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
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
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
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
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
111
1391
1396
10.1073/pnas.1309842111
24474763
Structure of an HIV-1-neutralizing antibody target, the lipid-bound gp41 envelope membrane proximal region trimer.
2014
10.2210/pdb2lp7/pdb
pdb_00002lp7
7010.809
Envelope glycoprotein
3
man
polymer
no
no
GYIPEAPRDGQAYVRKDGEWVLLSTFLGSSGNEQELLELDKWASLWNWFNITNWLWYIK
GYIPEAPRDGQAYVRKDGEWVLLSTFLGSSGNEQELLELDKWASLWNWFNITNWLWYIK
A,B,C
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
sample
11676
Human immunodeficiency virus 1
562
Escherichia coli
pTCLE
database_2
pdbx_database_status
pdbx_nmr_software
pdbx_nmr_spectrometer
repository
Initial release
Database references
Database references
Data collection
Database references
Other
1
0
2013-02-06
1
1
2014-01-15
1
2
2014-03-05
1
3
2023-06-14
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_nmr_data
_pdbx_nmr_software.name
_pdbx_nmr_spectrometer.model
BMRB
Y
RCSB
2012-02-03
REL
REL
REL
REL
structures with the least restraint violations
400
11
2D 1H-15N HSQC
3D HNCA
3D HNCACB
3D HN(CO)CA
3D 1H-15N NOESY
50
mM
100
mM
[U-99% 2H]
6.0
ambient
30
K
simulated annealing
1
lowest energy
50 mM sodium phosphate, 100 mM [U-99% 2H] DPC, 90% H2O/10% D2O
90% H2O/10% D2O
Schwieters, Kuszewski, Tjandra and Clore
structure solution
X-PLOR NIH
Schwieters, Kuszewski, Tjandra and Clore
refinement
X-PLOR NIH
800
Varian
INOVA
Varian INOVA
600
Varian
INOVA
Varian INOVA
950
Bruker
AVANCE
Bruker Avance
GLY
1
n
1
GLY
1
A
TYR
2
n
2
TYR
2
A
ILE
3
n
3
ILE
3
A
PRO
4
n
4
PRO
4
A
GLU
5
n
5
GLU
5
A
ALA
6
n
6
ALA
6
A
PRO
7
n
7
PRO
7
A
ARG
8
n
8
ARG
8
A
ASP
9
n
9
ASP
9
A
GLY
10
n
10
GLY
10
A
GLN
11
n
11
GLN
11
A
ALA
12
n
12
ALA
12
A
TYR
13
n
13
TYR
13
A
VAL
14
n
14
VAL
14
A
ARG
15
n
15
ARG
15
A
LYS
16
n
16
LYS
16
A
ASP
17
n
17
ASP
17
A
GLY
18
n
18
GLY
18
A
GLU
19
n
19
GLU
19
A
TRP
20
n
20
TRP
20
A
VAL
21
n
21
VAL
21
A
LEU
22
n
22
LEU
22
A
LEU
23
n
23
LEU
23
A
SER
24
n
24
SER
24
A
THR
25
n
25
THR
25
A
PHE
26
n
26
PHE
26
A
LEU
27
n
27
LEU
27
A
GLY
28
n
28
GLY
28
A
SER
29
n
29
SER
29
A
SER
30
n
30
SER
30
A
GLY
31
n
31
GLY
31
A
ASN
32
n
32
ASN
32
A
GLU
33
n
33
GLU
33
A
GLN
34
n
34
GLN
34
A
GLU
35
n
35
GLU
35
A
LEU
36
n
36
LEU
36
A
LEU
37
n
37
LEU
37
A
GLU
38
n
38
GLU
38
A
LEU
39
n
39
LEU
39
A
ASP
40
n
40
ASP
40
A
LYS
41
n
41
LYS
41
A
TRP
42
n
42
TRP
42
A
ALA
43
n
43
ALA
43
A
SER
44
n
44
SER
44
A
LEU
45
n
45
LEU
45
A
TRP
46
n
46
TRP
46
A
ASN
47
n
47
ASN
47
A
TRP
48
n
48
TRP
48
A
PHE
49
n
49
PHE
49
A
ASN
50
n
50
ASN
50
A
ILE
51
n
51
ILE
51
A
THR
52
n
52
THR
52
A
ASN
53
n
53
ASN
53
A
TRP
54
n
54
TRP
54
A
LEU
55
n
55
LEU
55
A
TRP
56
n
56
TRP
56
A
TYR
57
n
57
TYR
57
A
ILE
58
n
58
ILE
58
A
LYS
59
n
59
LYS
59
A
GLY
1
n
1
GLY
1
B
TYR
2
n
2
TYR
2
B
ILE
3
n
3
ILE
3
B
PRO
4
n
4
PRO
4
B
GLU
5
n
5
GLU
5
B
ALA
6
n
6
ALA
6
B
PRO
7
n
7
PRO
7
B
ARG
8
n
8
ARG
8
B
ASP
9
n
9
ASP
9
B
GLY
10
n
10
GLY
10
B
GLN
11
n
11
GLN
11
B
ALA
12
n
12
ALA
12
B
TYR
13
n
13
TYR
13
B
VAL
14
n
14
VAL
14
B
ARG
15
n
15
ARG
15
B
LYS
16
n
16
LYS
16
B
ASP
17
n
17
ASP
17
B
GLY
18
n
18
GLY
18
B
GLU
19
n
19
GLU
19
B
TRP
20
n
20
TRP
20
B
VAL
21
n
21
VAL
21
B
LEU
22
n
22
LEU
22
B
LEU
23
n
23
LEU
23
B
SER
24
n
24
SER
24
B
THR
25
n
25
THR
25
B
PHE
26
n
26
PHE
26
B
LEU
27
n
27
LEU
27
B
GLY
28
n
28
GLY
28
B
SER
29
n
29
SER
29
B
SER
30
n
30
SER
30
B
GLY
31
n
31
GLY
31
B
ASN
32
n
32
ASN
32
B
GLU
33
n
33
GLU
33
B
GLN
34
n
34
GLN
34
B
GLU
35
n
35
GLU
35
B
LEU
36
n
36
LEU
36
B
LEU
37
n
37
LEU
37
B
GLU
38
n
38
GLU
38
B
LEU
39
n
39
LEU
39
B
ASP
40
n
40
ASP
40
B
LYS
41
n
41
LYS
41
B
TRP
42
n
42
TRP
42
B
ALA
43
n
43
ALA
43
B
SER
44
n
44
SER
44
B
LEU
45
n
45
LEU
45
B
TRP
46
n
46
TRP
46
B
ASN
47
n
47
ASN
47
B
TRP
48
n
48
TRP
48
B
PHE
49
n
49
PHE
49
B
ASN
50
n
50
ASN
50
B
ILE
51
n
51
ILE
51
B
THR
52
n
52
THR
52
B
ASN
53
n
53
ASN
53
B
TRP
54
n
54
TRP
54
B
LEU
55
n
55
LEU
55
B
TRP
56
n
56
TRP
56
B
TYR
57
n
57
TYR
57
B
ILE
58
n
58
ILE
58
B
LYS
59
n
59
LYS
59
B
GLY
1
n
1
GLY
1
C
TYR
2
n
2
TYR
2
C
ILE
3
n
3
ILE
3
C
PRO
4
n
4
PRO
4
C
GLU
5
n
5
GLU
5
C
ALA
6
n
6
ALA
6
C
PRO
7
n
7
PRO
7
C
ARG
8
n
8
ARG
8
C
ASP
9
n
9
ASP
9
C
GLY
10
n
10
GLY
10
C
GLN
11
n
11
GLN
11
C
ALA
12
n
12
ALA
12
C
TYR
13
n
13
TYR
13
C
VAL
14
n
14
VAL
14
C
ARG
15
n
15
ARG
15
C
LYS
16
n
16
LYS
16
C
ASP
17
n
17
ASP
17
C
GLY
18
n
18
GLY
18
C
GLU
19
n
19
GLU
19
C
TRP
20
n
20
TRP
20
C
VAL
21
n
21
VAL
21
C
LEU
22
n
22
LEU
22
C
LEU
23
n
23
LEU
23
C
SER
24
n
24
SER
24
C
THR
25
n
25
THR
25
C
PHE
26
n
26
PHE
26
C
LEU
27
n
27
LEU
27
C
GLY
28
n
28
GLY
28
C
SER
29
n
29
SER
29
C
SER
30
n
30
SER
30
C
GLY
31
n
31
GLY
31
C
ASN
32
n
32
ASN
32
C
GLU
33
n
33
GLU
33
C
GLN
34
n
34
GLN
34
C
GLU
35
n
35
GLU
35
C
LEU
36
n
36
LEU
36
C
LEU
37
n
37
LEU
37
C
GLU
38
n
38
GLU
38
C
LEU
39
n
39
LEU
39
C
ASP
40
n
40
ASP
40
C
LYS
41
n
41
LYS
41
C
TRP
42
n
42
TRP
42
C
ALA
43
n
43
ALA
43
C
SER
44
n
44
SER
44
C
LEU
45
n
45
LEU
45
C
TRP
46
n
46
TRP
46
C
ASN
47
n
47
ASN
47
C
TRP
48
n
48
TRP
48
C
PHE
49
n
49
PHE
49
C
ASN
50
n
50
ASN
50
C
ILE
51
n
51
ILE
51
C
THR
52
n
52
THR
52
C
ASN
53
n
53
ASN
53
C
TRP
54
n
54
TRP
54
C
LEU
55
n
55
LEU
55
C
TRP
56
n
56
TRP
56
C
TYR
57
n
57
TYR
57
C
ILE
58
n
58
ILE
58
C
LYS
59
n
59
LYS
59
C
author_defined_assembly
3
trimeric
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
B
O
GLU
19
B
O
GLU
19
B
N
LYS
16
B
N
LYS
16
B
O
ARG
15
B
O
ARG
15
A
N
TYR
13
A
N
TYR
13
A
N
VAL
14
A
N
VAL
14
A
O
VAL
21
A
O
VAL
21
A
O
VAL
21
A
O
VAL
21
A
N
VAL
14
A
N
VAL
14
A
N
ARG
15
A
N
ARG
15
C
O
TYR
13
C
O
TYR
13
C
N
LYS
16
C
N
LYS
16
C
O
GLU
19
C
O
GLU
19
C
O
ARG
15
C
O
ARG
15
B
N
TYR
13
B
N
TYR
13
4
B
B
O
H
LEU
TRP
45
48
1.58
8
B
B
H1
H
GLY
TYR
1
2
1.31
9
C
C
H3
H
GLY
TYR
1
2
1.33
9
C
C
O
H
LEU
PHE
23
26
1.59
11
B
B
O
H
LEU
TRP
45
48
1.59
1
A
ILE
3
-157.81
51.93
1
A
GLU
5
172.37
107.87
1
A
ASN
32
-162.61
-5.94
1
B
PRO
4
-44.82
-75.48
1
B
GLU
5
162.45
-29.64
1
B
ALA
6
74.48
144.62
1
B
ASP
9
-140.48
10.64
1
B
ASP
17
38.33
41.60
1
B
SER
29
-160.06
56.37
1
B
SER
30
-162.91
86.48
1
B
ASN
32
-161.26
-14.54
1
B
PHE
49
-60.65
7.01
1
C
ASP
17
38.55
38.81
1
C
SER
29
45.54
102.25
1
C
SER
30
79.22
-24.78
1
C
ASN
32
-162.13
-8.13
2
A
ILE
3
51.92
95.36
2
A
GLU
5
164.46
131.13
2
A
SER
29
-79.44
-169.80
2
A
SER
30
78.28
-48.90
2
A
ASN
32
-74.90
27.40
2
B
ILE
3
60.57
88.42
2
B
PRO
4
-49.40
-178.37
2
B
GLU
5
-61.75
-145.23
2
B
ASP
17
37.89
44.11
2
B
SER
30
42.92
22.22
2
B
ASN
32
-164.31
-8.29
2
B
PHE
49
-64.38
6.58
2
C
ILE
3
47.72
74.03
2
C
PRO
7
-54.06
99.91
2
C
ASP
17
37.60
37.02
2
C
SER
29
54.61
154.17
2
C
SER
30
42.90
22.15
2
C
ASN
32
81.07
-6.16
2
C
LEU
36
-67.35
0.87
2
C
PHE
49
-46.37
-18.26
3
A
ILE
3
56.04
71.72
3
A
GLU
5
-62.39
-147.88
3
A
SER
30
78.55
-35.66
3
A
ASN
32
-75.14
26.88
3
B
TYR
2
-147.19
-132.77
3
B
PRO
4
-67.14
-85.46
3
B
GLU
5
169.83
115.01
3
B
ASP
17
38.31
42.30
3
B
ASN
32
-163.91
-6.22
3
C
ILE
3
43.95
72.62
3
C
PRO
4
-54.47
172.81
3
C
GLU
5
-55.95
170.02
3
C
ASN
32
-163.84
-7.45
4
A
ALA
6
155.26
-38.89
4
A
PRO
7
-66.73
59.12
4
A
ARG
8
-103.53
75.07
4
A
SER
29
42.10
94.21
4
A
SER
30
77.14
-30.78
4
A
ASN
32
-161.60
-12.82
4
B
GLU
5
178.06
-43.34
4
B
ALA
6
74.79
94.92
4
B
PRO
7
-47.60
176.75
4
B
ASP
17
39.31
43.45
4
B
SER
30
78.31
-26.74
4
B
ASN
32
-163.00
-13.51
4
B
PHE
49
-45.16
-18.17
4
C
TYR
2
47.42
72.38
4
C
GLU
5
-179.13
-107.63
4
C
ALA
6
67.71
70.02
4
C
ASP
9
-152.29
3.05
4
C
ASP
17
38.35
40.16
4
C
SER
29
53.09
112.17
4
C
SER
30
78.89
-27.69
4
C
ASN
32
-162.93
-13.37
4
C
PHE
49
-67.26
7.79
5
A
ILE
3
52.55
70.96
5
A
GLU
5
-59.97
-179.80
5
A
ASP
17
39.17
47.06
5
A
SER
29
-79.63
-163.90
5
A
SER
30
77.90
-36.40
5
A
ASN
32
-74.82
25.27
5
A
PHE
49
-65.47
7.58
5
B
TYR
2
-45.49
165.53
5
B
PRO
4
-46.98
164.83
5
B
GLU
5
-51.25
-179.51
5
B
SER
29
-159.83
-127.83
5
B
SER
30
77.71
-35.38
5
B
PHE
49
-45.43
-18.12
5
C
TYR
2
-153.67
1.37
5
C
PRO
4
-51.90
173.73
5
C
GLU
5
-52.51
179.34
5
C
ASP
17
39.31
45.22
5
C
SER
29
-79.92
-141.03
6
A
ILE
3
-36.76
130.98
6
A
GLU
5
-165.39
-130.85
6
A
ALA
6
171.92
76.53
6
A
PRO
7
-49.38
155.13
6
A
ASP
17
39.44
44.11
6
A
SER
30
80.30
-68.60
6
A
ASN
32
-163.81
-7.00
6
B
ILE
3
17.37
70.08
6
B
GLU
5
-169.39
-132.98
6
B
ALA
6
171.49
78.72
6
B
ASP
17
37.84
41.68
6
B
SER
29
-79.33
-169.06
6
B
SER
30
77.59
-36.40
6
B
ASN
32
-75.40
27.31
6
B
PHE
49
-67.57
7.59
6
C
PRO
4
-43.60
-76.02
6
C
GLU
5
173.22
-27.19
6
C
ALA
6
74.76
144.84
6
C
ASP
17
38.10
41.97
6
C
SER
29
-79.18
-168.70
6
C
SER
30
78.12
-37.12
6
C
ASN
32
-75.39
28.66
7
A
TYR
2
47.40
91.51
7
A
GLU
5
-163.19
101.92
7
A
ASP
17
38.46
43.67
7
A
SER
30
-162.25
-23.56
7
B
TYR
2
-150.90
-158.45
7
B
PRO
4
-77.69
-162.45
7
B
GLU
5
61.93
150.17
7
B
ALA
6
179.50
74.18
7
B
PRO
7
-47.16
151.92
7
B
ASP
17
37.35
40.84
7
B
LEU
27
-73.95
-75.62
7
B
SER
29
41.19
89.51
7
B
SER
30
76.13
-27.37
7
B
ASN
32
-160.90
-12.08
7
B
PHE
49
-45.07
-19.09
7
C
ILE
3
52.12
97.52
7
C
PRO
4
-45.23
-71.70
7
C
GLU
5
171.94
126.67
7
C
ASP
17
39.75
38.60
7
C
SER
29
58.03
138.40
7
C
ASN
32
-161.93
-20.48
7
C
PHE
49
-45.05
-19.47
8
A
TYR
2
-146.12
36.92
8
A
PRO
4
-55.70
93.68
8
A
GLU
5
179.72
96.98
8
A
ASN
32
-163.28
-6.63
8
B
GLU
5
-179.77
-39.77
8
B
ALA
6
73.57
86.54
8
B
PRO
7
-50.14
-175.88
8
B
ASP
17
38.67
40.13
8
B
SER
30
80.34
2.61
8
B
ASN
32
-164.62
-5.30
8
C
TYR
2
-148.20
-5.24
8
C
GLU
5
-174.95
-118.20
8
C
ALA
6
166.40
84.96
8
C
PRO
7
-48.71
150.03
8
C
ASP
17
39.25
36.33
8
C
SER
30
78.42
-34.21
8
C
ASN
32
-75.46
27.26
9
A
TYR
2
-144.86
-127.11
9
A
GLU
5
-170.41
119.66
9
A
ALA
6
-153.55
-45.04
9
A
ASP
9
-150.66
14.18
9
A
ASP
17
39.85
46.69
9
A
SER
30
79.07
-36.32
9
A
ASN
32
-75.59
31.61
9
B
TYR
2
53.83
171.84
9
B
ILE
3
44.33
74.17
9
B
PRO
4
-54.79
-140.16
9
B
GLU
5
-107.19
-169.32
9
B
ALA
6
-167.93
72.37
9
B
ASP
17
39.37
40.57
9
B
SER
30
78.59
-37.90
9
B
ASN
32
-75.18
28.38
9
B
PHE
49
-45.87
-17.52
9
C
ILE
3
58.78
95.44
9
C
PRO
4
-45.06
-70.40
9
C
GLU
5
170.92
128.08
9
C
ASP
17
38.84
41.75
9
C
SER
30
79.04
-42.54
9
C
ASN
32
-74.44
30.65
10
A
PRO
4
-66.86
-72.95
10
A
GLU
5
176.89
-37.08
10
A
ALA
6
62.55
149.86
10
A
ASP
17
39.78
42.15
10
A
SER
29
54.37
129.91
10
A
ASN
32
-161.21
-14.71
10
B
TYR
13
-140.62
-151.11
10
B
ASP
17
39.60
43.25
10
B
SER
30
-163.82
-42.93
10
B
ASN
32
-76.41
22.71
10
C
PRO
4
-43.41
-72.84
10
C
GLU
5
165.46
121.50
10
C
ASP
17
38.68
43.30
10
C
SER
30
77.24
-0.36
10
C
ASN
32
-163.68
-4.42
11
A
TYR
2
-153.16
12.88
11
A
PRO
4
-61.22
-173.38
11
A
GLU
5
67.24
140.64
11
A
ALA
6
179.03
74.72
11
A
ASN
32
-162.98
-13.04
11
B
GLU
5
-170.77
-106.57
11
B
ALA
6
73.46
144.32
11
B
ASP
17
39.59
45.75
11
B
ASN
32
-162.20
-9.28
11
B
PHE
49
-45.31
-17.92
11
C
TYR
2
-150.11
-28.81
11
C
GLU
5
-52.47
178.48
11
C
ASP
17
38.49
45.62
11
C
SER
29
48.59
-111.03
11
C
ASN
32
-163.29
-16.86
lowest energy, model 8
Structure of gp41-M-MAT, a membrane associated MPER trimer from HIV-1 gp41.
1
N
N
1
N
N
1
N
N
A
LEU
23
A
LEU
23
HELX_P
A
GLY
28
A
GLY
28
1
1
6
A
ASN
32
A
ASN
32
HELX_P
A
PHE
49
A
PHE
49
1
2
18
A
PHE
49
A
PHE
49
HELX_P
A
LYS
59
A
LYS
59
1
3
11
B
LEU
23
B
LEU
23
HELX_P
B
GLY
28
B
GLY
28
1
4
6
B
ASN
32
B
ASN
32
HELX_P
B
PHE
49
B
PHE
49
1
5
18
B
PHE
49
B
PHE
49
HELX_P
B
LYS
59
B
LYS
59
1
6
11
C
LEU
22
C
LEU
22
HELX_P
C
GLY
28
C
GLY
28
1
7
7
C
ASN
32
C
ASN
32
HELX_P
C
PHE
49
C
PHE
49
1
8
18
C
ASN
50
C
ASN
50
HELX_P
C
LYS
59
C
LYS
59
1
9
10
VIRAL PROTEIN
gp41, VIRAL PROTEIN
2LP7
PDB
1
2LP7
1
59
2LP7
1
59
2LP7
A
1
1
59
1
59
2LP7
1
59
2LP7
B
1
1
59
1
59
2LP7
1
59
2LP7
C
1
1
59
7
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
B
GLU
19
B
GLU
19
B
VAL
21
B
VAL
21
B
ALA
12
B
ALA
12
B
LYS
16
B
LYS
16
A
ALA
12
A
ALA
12
A
LYS
16
A
LYS
16
A
GLU
19
A
GLU
19
A
LEU
22
A
LEU
22
A
ALA
12
A
ALA
12
A
LYS
16
A
LYS
16
C
ALA
12
C
ALA
12
C
LYS
16
C
LYS
16
C
GLU
19
C
GLU
19
C
VAL
21
C
VAL
21
C
ALA
12
C
ALA
12
C
LYS
16
C
LYS
16
B
ALA
12
B
ALA
12
B
LYS
16
B
LYS
16