0.023907
0.013803
0.000000
0.000000
0.027605
0.000000
0.000000
0.000000
0.011790
0.00000
0.00000
0.00000
Eckert, D.M.
Malashkevich, V.N.
Hong, L.H.
Carr, P.A.
Kim, P.S.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
41.829
41.829
84.817
C2 H4 O
44.053
ACETYL GROUP
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 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
Cl -1
35.453
CHLORIDE ION
non-polymer
C3 H7 N O2
89.093
D-ALANINE
D-peptide linking
C6 H15 N4 O2 1
175.209
D-ARGININE
D-peptide linking
C3 H7 N O2 S
121.158
D-CYSTEINE
D-peptide linking
C5 H9 N O4
147.129
D-GLUTAMIC ACID
D-peptide linking
C6 H10 N3 O2 1
156.162
D-HISTIDINE
D-peptide linking
C6 H13 N O2
131.173
D-LEUCINE
D-peptide linking
C11 H12 N2 O2
204.225
D-TRYPTOPHAN
D-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
H2 O
18.015
WATER
non-polymer
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
C5 H11 N O2 S
149.211
y
METHIONINE
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
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
US
Cell(Cambridge,Mass.)
CELLB5
0998
0092-8674
99
103
115
10.1016/S0092-8674(00)80066-5
10520998
Inhibiting HIV-1 entry: discovery of D-peptide inhibitors that target the gp41 coiled-coil pocket.
1999
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
284
859
865
Crystal structure of GCN4-pIQI, a trimeric coiled-coil with buried polar residues.
1998
US
Cell(Cambridge,Mass.)
CELLB5
0998
0092-8674
89
15613
15617
Core structure of gp41 from the HIV envelope glycoprotein
1997
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
IMAGE PLATE
1999-03-24
RIGAKU RAXIS
MAD
M
x-ray
1
1.1197
1.0
1.1393
1.0
1.1403
1.0
1.1399
1.0
X4A
NSLS
1.1197, 1.1393, 1.1403, 1.1399
SYNCHROTRON
NSLS BEAMLINE X4A
5468.566
FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GCN4-PIQI
HYDROPHOBIC POCKET
1
man
polymer
1859.119
D-PEPTIDE INHIBITOR
1
syn
polymer
35.453
CHLORIDE ION
1
syn
non-polymer
18.015
water
150
nat
water
IQN17
D10-P1
no
yes
(ACE)RMKQIEDKIEEIESKQKKIENEIARIKKLLQLTVWGIKQLQARIL
XRMKQIEDKIEEIESKQKKIENEIARIKKLLQLTVWGIKQLQARIL
A
polypeptide(L)
no
yes
(ACE)G(DAL)(DCY)(DGL)(DAL)(DAR)(DHI)(DAR)(DGL)(DTR)(DAL)(DTR)(DLE)(DCY)(DAL)
(DAL)
XGACEARHREWAWLCAA
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
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
baker's yeast,
Saccharomyces, Lentivirus
,
,
sample
4932,12721
Saccharomyces cerevisiae, Human immunodeficiency virus
1
2.7
53.7
VAPOR DIFFUSION, HANGING DROP
5.6
10% PEG 4000 0.1 M SODIUM CITRATE 20% 2-PROPANOL, pH 5.6, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
1
0
1999-10-13
1
1
2008-04-27
1
2
2011-07-13
RCSB
Y
RCSB
1999-09-06
REL
CL
CHLORIDE ION
HOH
water
THIS PEPTIDE WAS CHEMICALLY SYNTHESIZED
sample
CL
1
3
CL
CL
1001
A
WAT
1
4
HOH
HOH
1002
A
WAT
2
4
HOH
HOH
1003
A
WAT
3
4
HOH
HOH
1004
A
WAT
4
4
HOH
HOH
1005
A
WAT
5
4
HOH
HOH
1006
A
WAT
6
4
HOH
HOH
1007
A
WAT
7
4
HOH
HOH
1008
A
WAT
8
4
HOH
HOH
1009
A
WAT
9
4
HOH
HOH
1010
A
WAT
10
4
HOH
HOH
1011
A
WAT
11
4
HOH
HOH
1012
A
WAT
12
4
HOH
HOH
1013
A
WAT
13
4
HOH
HOH
1014
A
WAT
14
4
HOH
HOH
1015
A
WAT
15
4
HOH
HOH
1016
A
WAT
16
4
HOH
HOH
1017
A
WAT
17
4
HOH
HOH
1018
A
WAT
18
4
HOH
HOH
1019
A
WAT
19
4
HOH
HOH
1020
A
WAT
20
4
HOH
HOH
1021
A
WAT
21
4
HOH
HOH
1022
A
WAT
22
4
HOH
HOH
1023
A
WAT
23
4
HOH
HOH
1024
A
WAT
24
4
HOH
HOH
1025
A
WAT
25
4
HOH
HOH
1026
A
WAT
26
4
HOH
HOH
1027
A
WAT
28
4
HOH
HOH
1028
A
WAT
29
4
HOH
HOH
1029
A
WAT
30
4
HOH
HOH
1030
A
WAT
31
4
HOH
HOH
1031
A
WAT
32
4
HOH
HOH
1032
A
WAT
33
4
HOH
HOH
1033
A
WAT
34
4
HOH
HOH
1034
A
WAT
35
4
HOH
HOH
1035
A
WAT
36
4
HOH
HOH
1036
A
WAT
37
4
HOH
HOH
1037
A
WAT
38
4
HOH
HOH
1038
A
WAT
39
4
HOH
HOH
1039
A
WAT
40
4
HOH
HOH
1040
A
WAT
41
4
HOH
HOH
1041
A
WAT
42
4
HOH
HOH
1042
A
WAT
43
4
HOH
HOH
1043
A
WAT
44
4
HOH
HOH
1044
A
WAT
45
4
HOH
HOH
1045
A
WAT
46
4
HOH
HOH
1046
A
WAT
48
4
HOH
HOH
1047
A
WAT
49
4
HOH
HOH
1048
A
WAT
50
4
HOH
HOH
1049
A
WAT
51
4
HOH
HOH
1050
A
WAT
53
4
HOH
HOH
1051
A
WAT
54
4
HOH
HOH
1052
A
WAT
55
4
HOH
HOH
1053
A
WAT
57
4
HOH
HOH
1054
A
WAT
58
4
HOH
HOH
1055
A
WAT
59
4
HOH
HOH
1056
A
WAT
60
4
HOH
HOH
1057
A
WAT
61
4
HOH
HOH
1058
A
WAT
62
4
HOH
HOH
1059
A
WAT
63
4
HOH
HOH
1060
A
WAT
64
4
HOH
HOH
1061
A
WAT
66
4
HOH
HOH
1062
A
WAT
68
4
HOH
HOH
1063
A
WAT
69
4
HOH
HOH
1064
A
WAT
70
4
HOH
HOH
1065
A
WAT
76
4
HOH
HOH
1066
A
WAT
77
4
HOH
HOH
1067
A
WAT
80
4
HOH
HOH
1068
A
WAT
90
4
HOH
HOH
1069
A
WAT
91
4
HOH
HOH
1070
A
WAT
92
4
HOH
HOH
1071
A
WAT
93
4
HOH
HOH
1072
A
WAT
94
4
HOH
HOH
1073
A
WAT
95
4
HOH
HOH
1074
A
WAT
96
4
HOH
HOH
1075
A
WAT
97
4
HOH
HOH
1076
A
WAT
98
4
HOH
HOH
1077
A
WAT
99
4
HOH
HOH
1078
A
WAT
100
4
HOH
HOH
1079
A
WAT
101
4
HOH
HOH
1080
A
WAT
102
4
HOH
HOH
1081
A
WAT
103
4
HOH
HOH
1082
A
WAT
104
4
HOH
HOH
1083
A
WAT
105
4
HOH
HOH
1084
A
WAT
106
4
HOH
HOH
1085
A
WAT
107
4
HOH
HOH
1086
A
WAT
108
4
HOH
HOH
1087
A
WAT
109
4
HOH
HOH
1088
A
WAT
110
4
HOH
HOH
1089
A
WAT
114
4
HOH
HOH
1090
A
WAT
115
4
HOH
HOH
1091
A
WAT
117
4
HOH
HOH
1092
A
WAT
118
4
HOH
HOH
1093
A
WAT
119
4
HOH
HOH
1094
A
WAT
120
4
HOH
HOH
1095
A
WAT
121
4
HOH
HOH
1096
A
WAT
122
4
HOH
HOH
1097
A
WAT
123
4
HOH
HOH
1098
A
WAT
124
4
HOH
HOH
1099
A
WAT
125
4
HOH
HOH
1100
A
WAT
127
4
HOH
HOH
1101
A
WAT
128
4
HOH
HOH
1102
A
WAT
129
4
HOH
HOH
1103
A
WAT
130
4
HOH
HOH
1104
A
WAT
131
4
HOH
HOH
1105
A
WAT
132
4
HOH
HOH
1106
A
WAT
133
4
HOH
HOH
1107
A
WAT
134
4
HOH
HOH
1108
A
WAT
135
4
HOH
HOH
1109
A
WAT
136
4
HOH
HOH
1110
A
WAT
137
4
HOH
HOH
1111
A
WAT
138
4
HOH
HOH
1112
A
WAT
139
4
HOH
HOH
1113
A
WAT
144
4
HOH
HOH
1114
A
WAT
145
4
HOH
HOH
1115
A
WAT
146
4
HOH
HOH
1116
A
WAT
149
4
HOH
HOH
1117
A
WAT
150
4
HOH
HOH
1118
A
WAT
47
4
HOH
HOH
47
D
WAT
52
4
HOH
HOH
52
D
WAT
56
4
HOH
HOH
56
D
WAT
65
4
HOH
HOH
65
D
WAT
67
4
HOH
HOH
67
D
WAT
71
4
HOH
HOH
71
D
WAT
72
4
HOH
HOH
72
D
WAT
73
4
HOH
HOH
73
D
WAT
74
4
HOH
HOH
74
D
WAT
75
4
HOH
HOH
75
D
WAT
78
4
HOH
HOH
78
D
WAT
79
4
HOH
HOH
79
D
WAT
81
4
HOH
HOH
81
D
WAT
82
4
HOH
HOH
82
D
WAT
83
4
HOH
HOH
83
D
WAT
84
4
HOH
HOH
84
D
WAT
85
4
HOH
HOH
85
D
WAT
86
4
HOH
HOH
86
D
WAT
87
4
HOH
HOH
87
D
WAT
88
4
HOH
HOH
88
D
WAT
89
4
HOH
HOH
89
D
WAT
111
4
HOH
HOH
111
D
WAT
112
4
HOH
HOH
112
D
WAT
113
4
HOH
HOH
113
D
WAT
116
4
HOH
HOH
116
D
WAT
126
4
HOH
HOH
126
D
WAT
140
4
HOH
HOH
140
D
WAT
141
4
HOH
HOH
141
D
WAT
142
4
HOH
HOH
142
D
WAT
143
4
HOH
HOH
143
D
WAT
147
4
HOH
HOH
147
D
WAT
148
4
HOH
HOH
148
D
WAT
151
4
HOH
HOH
151
D
ACE
0
n
1
ACE
0
A
ARG
1
n
2
ARG
1
A
MET
2
n
3
MET
2
A
LYS
3
n
4
LYS
3
A
GLN
4
n
5
GLN
4
A
ILE
5
n
6
ILE
5
A
GLU
6
n
7
GLU
6
A
ASP
7
n
8
ASP
7
A
LYS
8
n
9
LYS
8
A
ILE
9
n
10
ILE
9
A
GLU
10
n
11
GLU
10
A
GLU
11
n
12
GLU
11
A
ILE
12
n
13
ILE
12
A
GLU
13
n
14
GLU
13
A
SER
14
n
15
SER
14
A
LYS
15
n
16
LYS
15
A
GLN
16
n
17
GLN
16
A
LYS
17
n
18
LYS
17
A
LYS
18
n
19
LYS
18
A
ILE
19
n
20
ILE
19
A
GLU
20
n
21
GLU
20
A
ASN
21
n
22
ASN
21
A
GLU
22
n
23
GLU
22
A
ILE
23
n
24
ILE
23
A
ALA
24
n
25
ALA
24
A
ARG
25
n
26
ARG
25
A
ILE
26
n
27
ILE
26
A
LYS
27
n
28
LYS
27
A
LYS
28
n
29
LYS
28
A
LEU
29
n
30
LEU
29
A
LEU
30
n
31
LEU
30
A
GLN
31
n
32
GLN
31
A
LEU
32
n
33
LEU
32
A
THR
33
n
34
THR
33
A
VAL
34
n
35
VAL
34
A
TRP
35
n
36
TRP
35
A
GLY
36
n
37
GLY
36
A
ILE
37
n
38
ILE
37
A
LYS
38
n
39
LYS
38
A
GLN
39
n
40
GLN
39
A
LEU
40
n
41
LEU
40
A
GLN
41
n
42
GLN
41
A
ALA
42
n
43
ALA
42
A
ARG
43
n
44
ARG
43
A
ILE
44
n
45
ILE
44
A
LEU
45
n
46
LEU
45
A
ACE
0
n
1
ACE
0
D
DLY
1
n
2
GLY
1
D
DAL
2
n
3
DAL
2
D
DCY
3
n
4
DCY
3
D
DGL
4
n
5
DGL
4
D
DAL
5
n
6
DAL
5
D
DAR
6
n
7
DAR
6
D
DHI
7
n
8
DHI
7
D
DAR
8
n
9
DAR
8
D
DGL
9
n
10
DGL
9
D
DTR
10
n
11
DTR
10
D
DAL
11
n
12
DAL
11
D
DTR
12
n
13
DTR
12
D
DEU
13
n
14
DLE
13
D
DCY
14
n
15
DCY
14
D
DAL
15
n
16
DAL
15
D
DAL
16
n
17
DAL
16
D
author_and_software_defined_assembly
PISA,PQS
6
hexameric
9460
-115
10980
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
-0.5000000000
-0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_655
-y+1,x-y,z
crystal symmetry operation
41.8290000000
0.0000000000
0.0000000000
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_665
-x+y+1,-x+1,z
crystal symmetry operation
20.9145000000
36.2249766149
0.0000000000
1
A
CL
1001
C
CL
1
A
HOH
1020
D
HOH
1
A
HOH
1063
D
HOH
1
A
HOH
1088
D
HOH
1
A
HOH
1107
D
HOH
1
A
HOH
1109
D
HOH
1
-6.14
0.50
120.30
114.16
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
43
43
43
N
PROTEIN_REP_D.PARAM
PROTEIN.TOP
WATER_REP.PARA
WATER.TOP
ION.PARAM
ION.TOP
29.7
3.61
1.74
0.00
3.61
0.00
-7.22
0.245
0.007
0.214
0.214
0.214
1.50
10.00
1362
14322
13549
10.0
94.6
RANDOM
646169.44
0.00
1
RESTRAINED
THROUGHOUT
0.0
0.0
ENGH & HUBER
FLAT MODEL
58.34
0.394
0.20
0.18
5.00
0.12
0.09
1.50
10.00
150
666
1
0
515
0.012
1.5
15.7
1.00
0.956
2.0
1.503
3.0
1.853
3.0
2.676
3.5
0.27
0.018
0.233
1.59
219
2008
6
9.8
96.1
21.6
1.5
35.0
1CZQ
14503
13604
0.0
-3
0.048
1
16.8
6.5
93.8
0.235
1.5
1.55
4.5
1
6.1
86.8
data reduction
DENZO
data scaling
SCALEPACK
phasing
MLPHARE
refinement
CNS
0.5
FUSION PROTEIN BETWEEN THE HYDROPHOBIC POCKET OF HIV GP41 AND GCN4-PIQI
CRYSTAL STRUCTURE OF THE D10-P1/IQN17 COMPLEX: A D-PEPTIDE INHIBITOR OF HIV-1 ENTRY BOUND TO THE GP41 COILED-COIL POCKET.
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
A
ARG
1
A
ARG
2
HELX_P
A
LEU
45
A
LEU
46
1
1
45
disulf
2.048
D
DCY
3
B
SG
DCY
4
1_555
D
DCY
14
B
SG
DCY
15
1_555
covale
1.333
A
ACE
0
A
C
ACE
1
1_555
A
ARG
1
A
N
ARG
2
1_555
covale
1.336
D
ACE
0
B
C
ACE
1
1_555
D
GLY
1
B
N
GLY
2
1_555
covale
1.327
D
GLY
1
B
C
GLY
2
1_555
D
DAL
2
B
N
DAL
3
1_555
covale
1.324
D
DAL
2
B
C
DAL
3
1_555
D
DCY
3
B
N
DCY
4
1_555
covale
1.323
D
DCY
3
B
C
DCY
4
1_555
D
DGL
4
B
N
DGL
5
1_555
covale
2.048
D
DCY
3
B
SG
DCY
4
1_555
D
DCY
14
B
SG
DCY
15
1_555
covale
1.326
D
DGL
4
B
C
DGL
5
1_555
D
DAL
5
B
N
DAL
6
1_555
covale
1.327
D
DAL
5
B
C
DAL
6
1_555
D
DAR
6
B
N
DAR
7
1_555
covale
1.324
D
DAR
6
B
C
DAR
7
1_555
D
DHI
7
B
N
DHI
8
1_555
covale
1.329
D
DHI
7
B
C
DHI
8
1_555
D
DAR
8
B
N
DAR
9
1_555
covale
1.329
D
DAR
8
B
C
DAR
9
1_555
D
DGL
9
B
N
DGL
10
1_555
covale
1.328
D
DGL
9
B
C
DGL
10
1_555
D
DTR
10
B
N
DTR
11
1_555
covale
1.332
D
DTR
10
B
C
DTR
11
1_555
D
DAL
11
B
N
DAL
12
1_555
covale
1.335
D
DAL
11
B
C
DAL
12
1_555
D
DTR
12
B
N
DTR
13
1_555
covale
1.330
D
DTR
12
B
C
DTR
13
1_555
D
DLE
13
B
N
DLE
14
1_555
covale
1.335
D
DLE
13
B
C
DLE
14
1_555
D
DCY
14
B
N
DCY
15
1_555
covale
1.329
D
DCY
14
B
C
DCY
15
1_555
D
DAL
15
B
N
DAL
16
1_555
covale
1.332
D
DAL
15
B
C
DAL
16
1_555
D
DAL
16
B
N
DAL
17
1_555
Viral protein/inhibitor
ENVELOPE GLYCOPROTEIN, Viral protein-inhibitor COMPLEX
U36871
GB
1
1587615
1CZQ
PDB
2
1CZQ
565
581
1CZQ
29
45
1587615
A
1
30
46
0
16
1CZQ
0
16
1CZQ
D
2
1
17
BINDING SITE FOR RESIDUE CL A 1001
Software
3
BINDING SITE FOR CHAIN D OF D-PEPTIDE INHIBITOR
Software
34
A
GLN
16
A
GLN
17
3
1_555
A
GLN
16
A
GLN
17
3
3_665
A
GLN
16
A
GLN
17
3
2_655
A
LEU
32
A
LEU
33
34
1_555
A
VAL
34
A
VAL
35
34
2_655
A
TRP
35
A
TRP
36
34
1_555
A
LYS
38
A
LYS
39
34
2_655
A
GLN
41
A
GLN
42
34
2_655
A
ARG
43
A
ARG
44
34
5_556
A
ARG
43
A
ARG
44
34
6_656
A
ILE
44
A
ILE
45
34
6_656
A
LEU
45
A
LEU
46
34
6_656
A
HOH
1057
D
HOH
34
2_655
A
HOH
1065
D
HOH
34
2_655
A
HOH
1077
D
HOH
34
2_655
A
HOH
1083
D
HOH
34
5_556
A
HOH
1086
D
HOH
34
6_656
A
HOH
1106
D
HOH
34
4_546
A
HOH
1114
D
HOH
34
4_546
D
HOH
47
E
HOH
34
1_555
D
HOH
52
E
HOH
34
1_555
D
HOH
65
E
HOH
34
1_555
D
HOH
67
E
HOH
34
1_555
D
HOH
71
E
HOH
34
1_555
D
HOH
72
E
HOH
34
1_555
D
HOH
73
E
HOH
34
1_555
D
HOH
74
E
HOH
34
1_555
D
HOH
79
E
HOH
34
1_555
D
HOH
83
E
HOH
34
1_555
D
HOH
85
E
HOH
34
1_555
D
HOH
86
E
HOH
34
1_555
D
HOH
87
E
HOH
34
1_555
D
HOH
88
E
HOH
34
1_555
D
HOH
111
E
HOH
34
1_555
D
HOH
140
E
HOH
34
1_555
D
HOH
142
E
HOH
34
1_555
D
HOH
143
E
HOH
34
1_555
150
P 3 2 1