0.019268
0.000000
0.000000
0.000000
0.019268
0.000000
0.000000
0.000000
0.015773
0.00000
0.00000
0.00000
Vajdos, F.F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
51.900
51.900
63.400
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
C3 H7 N O2 S
121.158
y
CYSTEINE
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 H10 N3 O2 1
156.162
y
HISTIDINE
L-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
C5 H11 N O2 Se
196.106
n
SELENOMETHIONINE
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
Protein Sci.
PRCIEI
0795
0961-8368
6
2297
2307
9385632
Crystal structure of cyclophilin A complexed with a binding site peptide from the HIV-1 capsid protein.
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 AREA DETECTOR
1996-06
MARRESEARCH
SI(111)
M
x-ray
1
0.9794
1.0
X12C
NSLS
0.9794
SYNCHROTRON
NSLS BEAMLINE X12C
18092.887
CYCLOPHILIN A
5.2.1.8
SELENO-METHIONINE SUBSTITUTED
1
man
polymer
565.642
PEPTIDE FROM THE HIV-1 CAPSID PROTEIN
1
man
polymer
18.015
water
52
nat
water
no
yes
VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGF(MSE)CQGGDFTRHNGTGGKS
IYGEKFEDENFILKHTGPGILS(MSE)ANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEG(MSE)NIVEA(MSE)ERF
GSRNGKTSKKITIADCGQLE
VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGE
KFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADC
GQLE
A
polypeptide(L)
no
no
HAGPIA
HAGPIA
B
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
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
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
human
Homo
Escherichia
sample
CYTOPLASM
CYCLOPHILIN
9606
Homo sapiens
CYCLOPHILIN
562
Escherichia coli
1
2.29
46.22
8.4
pH 8.4
repository
Initial release
Version format compliance
Version format compliance
1
0
1998-03-18
1
1
2008-03-24
1
2
2011-07-13
Y
1997-10-04
REL
REL
HOH
water
HOH
201
3
HOH
HOH
201
A
HOH
202
3
HOH
HOH
202
A
HOH
203
3
HOH
HOH
203
A
HOH
204
3
HOH
HOH
204
A
HOH
205
3
HOH
HOH
205
A
HOH
206
3
HOH
HOH
206
A
HOH
207
3
HOH
HOH
207
A
HOH
208
3
HOH
HOH
208
A
HOH
209
3
HOH
HOH
209
A
HOH
210
3
HOH
HOH
210
A
HOH
211
3
HOH
HOH
211
A
HOH
212
3
HOH
HOH
212
A
HOH
214
3
HOH
HOH
214
A
HOH
215
3
HOH
HOH
215
A
HOH
216
3
HOH
HOH
216
A
HOH
217
3
HOH
HOH
217
A
HOH
218
3
HOH
HOH
218
A
HOH
219
3
HOH
HOH
219
A
HOH
220
3
HOH
HOH
220
A
HOH
221
3
HOH
HOH
221
A
HOH
222
3
HOH
HOH
222
A
HOH
223
3
HOH
HOH
223
A
HOH
224
3
HOH
HOH
224
A
HOH
225
3
HOH
HOH
225
A
HOH
226
3
HOH
HOH
226
A
HOH
227
3
HOH
HOH
227
A
HOH
228
3
HOH
HOH
228
A
HOH
229
3
HOH
HOH
229
A
HOH
230
3
HOH
HOH
230
A
HOH
231
3
HOH
HOH
231
A
HOH
232
3
HOH
HOH
232
A
HOH
233
3
HOH
HOH
233
A
HOH
234
3
HOH
HOH
234
A
HOH
235
3
HOH
HOH
235
A
HOH
236
3
HOH
HOH
236
A
HOH
237
3
HOH
HOH
237
A
HOH
238
3
HOH
HOH
238
A
HOH
239
3
HOH
HOH
239
A
HOH
240
3
HOH
HOH
240
A
HOH
241
3
HOH
HOH
241
A
HOH
242
3
HOH
HOH
242
A
HOH
243
3
HOH
HOH
243
A
HOH
244
3
HOH
HOH
244
A
HOH
245
3
HOH
HOH
245
A
HOH
246
3
HOH
HOH
246
A
HOH
248
3
HOH
HOH
248
A
HOH
249
3
HOH
HOH
249
A
HOH
250
3
HOH
HOH
250
A
HOH
251
3
HOH
HOH
251
A
HOH
252
3
HOH
HOH
252
A
HOH
213
3
HOH
HOH
213
B
HOH
247
3
HOH
HOH
247
B
VAL
1002
n
1
VAL
1002
A
ASN
1003
n
2
ASN
1003
A
PRO
1004
n
3
PRO
1004
A
THR
1005
n
4
THR
1005
A
VAL
1006
n
5
VAL
1006
A
PHE
1007
n
6
PHE
1007
A
PHE
1008
n
7
PHE
1008
A
ASP
1009
n
8
ASP
1009
A
ILE
1010
n
9
ILE
1010
A
ALA
1011
n
10
ALA
1011
A
VAL
1012
n
11
VAL
1012
A
ASP
1013
n
12
ASP
1013
A
GLY
1014
n
13
GLY
1014
A
GLU
1015
n
14
GLU
1015
A
PRO
1016
n
15
PRO
1016
A
LEU
1017
n
16
LEU
1017
A
GLY
1018
n
17
GLY
1018
A
ARG
1019
n
18
ARG
1019
A
VAL
1020
n
19
VAL
1020
A
SER
1021
n
20
SER
1021
A
PHE
1022
n
21
PHE
1022
A
GLU
1023
n
22
GLU
1023
A
LEU
1024
n
23
LEU
1024
A
PHE
1025
n
24
PHE
1025
A
ALA
1026
n
25
ALA
1026
A
ASP
1027
n
26
ASP
1027
A
LYS
1028
n
27
LYS
1028
A
VAL
1029
n
28
VAL
1029
A
PRO
1030
n
29
PRO
1030
A
LYS
1031
n
30
LYS
1031
A
THR
1032
n
31
THR
1032
A
ALA
1033
n
32
ALA
1033
A
GLU
1034
n
33
GLU
1034
A
ASN
1035
n
34
ASN
1035
A
PHE
1036
n
35
PHE
1036
A
ARG
1037
n
36
ARG
1037
A
ALA
1038
n
37
ALA
1038
A
LEU
1039
n
38
LEU
1039
A
SER
1040
n
39
SER
1040
A
THR
1041
n
40
THR
1041
A
GLY
1042
n
41
GLY
1042
A
GLU
1043
n
42
GLU
1043
A
LYS
1044
n
43
LYS
1044
A
GLY
1045
n
44
GLY
1045
A
PHE
1046
n
45
PHE
1046
A
GLY
1047
n
46
GLY
1047
A
TYR
1048
n
47
TYR
1048
A
LYS
1049
n
48
LYS
1049
A
GLY
1050
n
49
GLY
1050
A
SER
1051
n
50
SER
1051
A
CYS
1052
n
51
CYS
1052
A
PHE
1053
n
52
PHE
1053
A
HIS
1054
n
53
HIS
1054
A
ARG
1055
n
54
ARG
1055
A
ILE
1056
n
55
ILE
1056
A
ILE
1057
n
56
ILE
1057
A
PRO
1058
n
57
PRO
1058
A
GLY
1059
n
58
GLY
1059
A
PHE
1060
n
59
PHE
1060
A
MSE
1061
n
60
MSE
1061
A
CYS
1062
n
61
CYS
1062
A
GLN
1063
n
62
GLN
1063
A
GLY
1064
n
63
GLY
1064
A
GLY
1065
n
64
GLY
1065
A
ASP
1066
n
65
ASP
1066
A
PHE
1067
n
66
PHE
1067
A
THR
1068
n
67
THR
1068
A
ARG
1069
n
68
ARG
1069
A
HIS
1070
n
69
HIS
1070
A
ASN
1071
n
70
ASN
1071
A
GLY
1072
n
71
GLY
1072
A
THR
1073
n
72
THR
1073
A
GLY
1074
n
73
GLY
1074
A
GLY
1075
n
74
GLY
1075
A
LYS
1076
n
75
LYS
1076
A
SER
1077
n
76
SER
1077
A
ILE
1078
n
77
ILE
1078
A
TYR
1079
n
78
TYR
1079
A
GLY
1080
n
79
GLY
1080
A
GLU
1081
n
80
GLU
1081
A
LYS
1082
n
81
LYS
1082
A
PHE
1083
n
82
PHE
1083
A
GLU
1084
n
83
GLU
1084
A
ASP
1085
n
84
ASP
1085
A
GLU
1086
n
85
GLU
1086
A
ASN
1087
n
86
ASN
1087
A
PHE
1088
n
87
PHE
1088
A
ILE
1089
n
88
ILE
1089
A
LEU
1090
n
89
LEU
1090
A
LYS
1091
n
90
LYS
1091
A
HIS
1092
n
91
HIS
1092
A
THR
1093
n
92
THR
1093
A
GLY
1094
n
93
GLY
1094
A
PRO
1095
n
94
PRO
1095
A
GLY
1096
n
95
GLY
1096
A
ILE
1097
n
96
ILE
1097
A
LEU
1098
n
97
LEU
1098
A
SER
1099
n
98
SER
1099
A
MSE
1100
n
99
MSE
1100
A
ALA
1101
n
100
ALA
1101
A
ASN
1102
n
101
ASN
1102
A
ALA
1103
n
102
ALA
1103
A
GLY
1104
n
103
GLY
1104
A
PRO
1105
n
104
PRO
1105
A
ASN
1106
n
105
ASN
1106
A
THR
1107
n
106
THR
1107
A
ASN
1108
n
107
ASN
1108
A
GLY
1109
n
108
GLY
1109
A
SER
1110
n
109
SER
1110
A
GLN
1111
n
110
GLN
1111
A
PHE
1112
n
111
PHE
1112
A
PHE
1113
n
112
PHE
1113
A
ILE
1114
n
113
ILE
1114
A
CYS
1115
n
114
CYS
1115
A
THR
1116
n
115
THR
1116
A
ALA
1117
n
116
ALA
1117
A
LYS
1118
n
117
LYS
1118
A
THR
1119
n
118
THR
1119
A
GLU
1120
n
119
GLU
1120
A
TRP
1121
n
120
TRP
1121
A
LEU
1122
n
121
LEU
1122
A
ASP
1123
n
122
ASP
1123
A
GLY
1124
n
123
GLY
1124
A
LYS
1125
n
124
LYS
1125
A
HIS
1126
n
125
HIS
1126
A
VAL
1127
n
126
VAL
1127
A
VAL
1128
n
127
VAL
1128
A
PHE
1129
n
128
PHE
1129
A
GLY
1130
n
129
GLY
1130
A
LYS
1131
n
130
LYS
1131
A
VAL
1132
n
131
VAL
1132
A
LYS
1133
n
132
LYS
1133
A
GLU
1134
n
133
GLU
1134
A
GLY
1135
n
134
GLY
1135
A
MSE
1136
n
135
MSE
1136
A
ASN
1137
n
136
ASN
1137
A
ILE
1138
n
137
ILE
1138
A
VAL
1139
n
138
VAL
1139
A
GLU
1140
n
139
GLU
1140
A
ALA
1141
n
140
ALA
1141
A
MSE
1142
n
141
MSE
1142
A
GLU
1143
n
142
GLU
1143
A
ARG
1144
n
143
ARG
1144
A
PHE
1145
n
144
PHE
1145
A
GLY
1146
n
145
GLY
1146
A
SER
1147
n
146
SER
1147
A
ARG
1148
n
147
ARG
1148
A
ASN
1149
n
148
ASN
1149
A
GLY
1150
n
149
GLY
1150
A
LYS
1151
n
150
LYS
1151
A
THR
1152
n
151
THR
1152
A
SER
1153
n
152
SER
1153
A
LYS
1154
n
153
LYS
1154
A
LYS
1155
n
154
LYS
1155
A
ILE
1156
n
155
ILE
1156
A
THR
1157
n
156
THR
1157
A
ILE
1158
n
157
ILE
1158
A
ALA
1159
n
158
ALA
1159
A
ASP
1160
n
159
ASP
1160
A
CYS
1161
n
160
CYS
1161
A
GLY
1162
n
161
GLY
1162
A
GLN
1163
n
162
GLN
1163
A
LEU
1164
n
163
LEU
1164
A
GLU
1165
n
164
GLU
1165
A
HIS
1
n
1
HIS
1
B
ALA
2
n
2
ALA
2
B
GLY
3
n
3
GLY
3
B
PRO
4
n
4
PRO
4
B
ILE
5
n
5
ILE
5
B
ALA
6
n
6
ALA
6
B
author_and_software_defined_assembly
PISA
2
dimeric
740
-4
7490
A
MSE
1061
SELENOMETHIONINE
A
MSE
60
MET
A
MSE
1100
SELENOMETHIONINE
A
MSE
99
MET
A
MSE
1136
SELENOMETHIONINE
A
MSE
135
MET
A
MSE
1142
SELENOMETHIONINE
A
MSE
141
MET
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
O
ARG
1055
A
O
ARG
54
A
N
GLN
1063
A
N
GLN
62
A
O
CYS
1062
A
O
CYS
61
A
N
ILE
1114
A
N
ILE
113
A
O
PHE
1113
A
O
PHE
112
A
N
SER
1099
A
N
SER
98
A
O
LEU
1098
A
O
LEU
97
A
N
GLY
1130
A
N
GLY
129
A
O
LYS
1131
A
O
LYS
130
A
N
GLU
1023
A
N
GLU
22
A
O
GLU
1015
A
O
GLU
14
A
N
VAL
1012
A
N
VAL
11
A
O
PHE
1007
A
O
PHE
6
A
N
GLY
1162
A
N
GLY
161
1
A
VAL
1029
-113.20
70.82
1
A
PRO
1030
-51.84
-76.44
1
A
GLU
1043
-47.54
7.05
1
A
LYS
1044
-150.96
-4.07
1
A
PHE
1046
-100.62
-86.09
1
A
PHE
1060
-121.01
-77.52
1
A
ASN
1071
-134.86
-34.47
1
A
TYR
1079
-93.09
37.54
1
A
GLU
1081
-140.34
-63.00
1
A
ASN
1087
-174.98
-176.81
1
A
HIS
1092
-59.25
69.95
1
A
ALA
1101
-101.12
77.94
1
A
PRO
1105
-28.76
139.76
1
A
ALA
1117
174.37
161.96
1
A
PHE
1129
-147.98
-1.21
1
A
SER
1147
-154.23
-152.62
PARHCSDX.PRO
TOPHCSDX.PRO
TIP3P.PARAMETER
TIP3P.TOPOLOGY
26.5
BULK SOLVENT MODEL USED
THE PROTEIN IS SELENO-METHIONINE SUBSTITUTED, BUT THE
SELENO-METHIONINE RESIDUES WERE REFINED AS METHIONINES.
REGARDING THE HIGH R-VALUE: THIS IS THE STRUCTURE OF THE
COMPLEX REFINED IN A PSEUDO-SPACE GROUP. THE DETAILS ARE
ADDRESSED EXTENSIVELY IN THE PAPER. TO SUMMARIZE HERE, THE
HIGH R-VALUE FOR THIS STRUCTURE STEMS FROM THE BREAKDOWN IN
PSEUDO-SYMMETRY AT HIGH RESOLUTION.
0.3370000
0.019
0.2620000
0.2620000
2.55
15.00
304
5484
5.5
99.2
RANDOM
10000000.00
0.00100
1
RESTRAINED
THROUGHOUT
0.0
MAD
0.48
0.37
5.00
0.72
0.50
2.55
15.00
52
1350
40
0
1258
0.009
1.5
25.9
1.30
4.37
1.50
5.95
2.00
5.56
2.00
6.90
2.50
0.5060000
0.078
0.3810000
2.71
42
871
6
4.6
99.1
16.8
2.55
15.0
1AWS
5576
0.
0.0350000
1
19.1
97.6
2.55
2.59
0.0790000
95.7
model building
X-PLOR
3.843
refinement
X-PLOR
3.843
data reduction
DENZO
data scaling
SCALEPACK
phasing
X-PLOR
3.843
CYCLOPHILIN A, PEPTIDE FROM THE HIV-1 CAPSID PROTEIN
SECYPA COMPLEXED WITH HAGPIA (PSEUDO-SYMMETRIC MONOMER)
1
N
N
2
N
N
3
N
N
3
N
N
A
PRO
1030
A
PRO
29
HELX_P
A
THR
1041
A
THR
40
1
1
12
A
GLU
1120
A
GLU
119
HELX_P
A
LEU
1122
A
LEU
121
5
2
3
A
MSE
1136
A
MSE
135
HELX_P
A
ARG
1144
A
ARG
143
1
3
9
covale
1.338
A
MSE
1061
A
N
MSE
60
1_555
A
PHE
1060
A
C
PHE
59
1_555
covale
1.342
A
MSE
1061
A
C
MSE
60
1_555
A
CYS
1062
A
N
CYS
61
1_555
covale
1.324
A
MSE
1100
A
N
MSE
99
1_555
A
SER
1099
A
C
SER
98
1_555
covale
1.331
A
MSE
1100
A
C
MSE
99
1_555
A
ALA
1101
A
N
ALA
100
1_555
covale
1.331
A
MSE
1136
A
N
MSE
135
1_555
A
GLY
1135
A
C
GLY
134
1_555
covale
1.331
A
MSE
1136
A
C
MSE
135
1_555
A
ASN
1137
A
N
ASN
136
1_555
covale
1.336
A
MSE
1142
A
N
MSE
141
1_555
A
ALA
1141
A
C
ALA
140
1_555
covale
1.333
A
MSE
1142
A
C
MSE
141
1_555
A
GLU
1143
A
N
GLU
142
1_555
COMPLEX (ISOMERASE/PEPTIDE)
COMPLEX (ISOMERASE-PEPTIDE), CYCLOPHILIN A, HIV-1 CAPSID, PSEUDO-SYMMETRY, COMPLEX (ISOMERASE-PEPTIDE) complex
PPIA_HUMAN
UNP
1
1
P62937
VNPTVFFDIAVDGEPLGRVSFELFADKVPKTAENFRALSTGEKGFGYKGSCFHRIIPGFMCQGGDFTRHNGTGGKSIYGE
KFEDENFILKHTGPGILSMANAGPNTNGSQFFICTAKTEWLDGKHVVFGKVKEGMNIVEAMERFGSRNGKTSKKITIADC
GQLE
1AWS
PDB
2
1AWS
1
164
1AWS
1002
1165
P62937
A
1
1
164
1
6
1AWS
1
6
1AWS
B
2
1
6
1
MET
MODIFIED RESIDUE
MSE
1061
1AWS
A
P62937
UNP
60
60
1
MET
MODIFIED RESIDUE
MSE
1100
1AWS
A
P62937
UNP
99
99
1
MET
MODIFIED RESIDUE
MSE
1136
1AWS
A
P62937
UNP
135
135
1
MET
MODIFIED RESIDUE
MSE
1142
1AWS
A
P62937
UNP
141
141
8
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ARG
1055
A
ARG
54
A
ILE
1057
A
ILE
56
A
MSE
1061
A
MSE
60
A
GLY
1064
A
GLY
63
A
PHE
1112
A
PHE
111
A
CYS
1115
A
CYS
114
A
ILE
1097
A
ILE
96
A
MSE
1100
A
MSE
99
A
VAL
1128
A
VAL
127
A
GLU
1134
A
GLU
133
A
GLU
1015
A
GLU
14
A
LEU
1024
A
LEU
23
A
THR
1005
A
THR
4
A
VAL
1012
A
VAL
11
A
ILE
1156
A
ILE
155
A
GLN
1163
A
GLN
162
78
P 43