0.034698
0.000000
0.000000
0.000000
0.015237
0.000000
0.000000
0.000000
0.010761
0.000000
0.000000
0.000000
Tiefenbrunn, T.
Stout, C.D.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
8
90.000
90.000
90.000
28.820
65.630
92.930
C9 H7 N O2
161.157
1H-indole-6-carboxylic acid
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
C2 H6 O S
78.133
BETA-MERCAPTOETHANOL
non-polymer
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
C5 H10 O2
102.132
ISOVALERIC ACID
non-polymer
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
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C8 H17 N O3
175.225
STATINE
peptide-like
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
Acs Chem.Biol.
1554-8929
8
1223
1231
10.1021/cb300611p
23540839
Small molecule regulation of protein conformation by binding in the Flap of HIV protease.
2013
RESIDUES C ALA 5 AND C STA 6 ARE NOT PROPERLY LINKED.
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
100
1
Rh coated flat mirror
CCD
2010-06-11
ADSC QUANTUM 315r
Side scattering I-beam bent single crystal, asymmetric cut 4.9650 degrees
SINGLE WAVELENGTH
M
x-ray
1
0.979
1.0
BL7-1
SSRL
0.979
SYNCHROTRON
SSRL BEAMLINE BL7-1
10831.833
Protease
3.4.23.16
UNP residues 490-588
2
man
polymer
685.891
pepstatin
1
syn
polymer
78.133
BETA-MERCAPTOETHANOL
3
syn
non-polymer
161.157
1H-indole-6-carboxylic acid
1
syn
non-polymer
92.094
GLYCEROL
1
syn
non-polymer
18.015
water
165
nat
water
PR, Retropepsin
no
no
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
PQITLWKRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGRWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
A,B
polypeptide(L)
no
yes
(IVA)VV(STA)A(STA)
XVVXAX
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
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
R8
sample
pol
11676
Human immunodeficiency virus 1
469008
Escherichia coli
Rosetta2(DE3) pLysS
plasmid
pET-21a(+)
1
1.97
37.44
VAPOR DIFFUSION
6.5
0.2 M potassium bromide, 0.2 M potassium thiocyanate, 3% PGA-LM, 3% MPD, 10% DMSO, 0.1 M sodium cacodylate, pH 6.5, VAPOR DIFFUSION, temperature 298K
298
repository
Initial release
Database references
1
0
2013-05-01
1
1
2014-02-19
RCSB
Y
RCSB
2012-04-06
REL
REL
BME
BETA-MERCAPTOETHANOL
1F1
1H-indole-6-carboxylic acid
GOL
GLYCEROL
HOH
water
285516
Streptomyces argenteolus subsp. toyonakensis
sample
Enzyme inhibitor
Pepstatin
Oligopeptide
BME
4
3
BME
BME
101
A
1F1
46
4
1F1
1F1
102
A
GOL
1
5
GOL
GOL
101
B
BME
2
3
BME
BME
102
B
BME
3
3
BME
BME
103
B
HOH
10
6
HOH
HOH
201
A
HOH
11
6
HOH
HOH
202
A
HOH
12
6
HOH
HOH
203
A
HOH
13
6
HOH
HOH
204
A
HOH
16
6
HOH
HOH
205
A
HOH
17
6
HOH
HOH
206
A
HOH
18
6
HOH
HOH
207
A
HOH
19
6
HOH
HOH
208
A
HOH
21
6
HOH
HOH
209
A
HOH
22
6
HOH
HOH
210
A
HOH
23
6
HOH
HOH
211
A
HOH
24
6
HOH
HOH
212
A
HOH
30
6
HOH
HOH
213
A
HOH
31
6
HOH
HOH
214
A
HOH
33
6
HOH
HOH
215
A
HOH
35
6
HOH
HOH
216
A
HOH
38
6
HOH
HOH
217
A
HOH
40
6
HOH
HOH
218
A
HOH
41
6
HOH
HOH
219
A
HOH
42
6
HOH
HOH
220
A
HOH
43
6
HOH
HOH
221
A
HOH
45
6
HOH
HOH
222
A
HOH
48
6
HOH
HOH
223
A
HOH
51
6
HOH
HOH
224
A
HOH
55
6
HOH
HOH
225
A
HOH
58
6
HOH
HOH
226
A
HOH
61
6
HOH
HOH
227
A
HOH
62
6
HOH
HOH
228
A
HOH
63
6
HOH
HOH
229
A
HOH
67
6
HOH
HOH
230
A
HOH
68
6
HOH
HOH
231
A
HOH
71
6
HOH
HOH
232
A
HOH
74
6
HOH
HOH
233
A
HOH
75
6
HOH
HOH
234
A
HOH
76
6
HOH
HOH
235
A
HOH
77
6
HOH
HOH
236
A
HOH
79
6
HOH
HOH
237
A
HOH
81
6
HOH
HOH
238
A
HOH
82
6
HOH
HOH
239
A
HOH
83
6
HOH
HOH
240
A
HOH
90
6
HOH
HOH
241
A
HOH
93
6
HOH
HOH
242
A
HOH
96
6
HOH
HOH
243
A
HOH
97
6
HOH
HOH
244
A
HOH
98
6
HOH
HOH
245
A
HOH
102
6
HOH
HOH
246
A
HOH
104
6
HOH
HOH
247
A
HOH
108
6
HOH
HOH
248
A
HOH
109
6
HOH
HOH
249
A
HOH
111
6
HOH
HOH
250
A
HOH
116
6
HOH
HOH
251
A
HOH
119
6
HOH
HOH
252
A
HOH
120
6
HOH
HOH
253
A
HOH
121
6
HOH
HOH
254
A
HOH
123
6
HOH
HOH
255
A
HOH
125
6
HOH
HOH
256
A
HOH
129
6
HOH
HOH
257
A
HOH
131
6
HOH
HOH
258
A
HOH
134
6
HOH
HOH
259
A
HOH
135
6
HOH
HOH
260
A
HOH
136
6
HOH
HOH
261
A
HOH
138
6
HOH
HOH
262
A
HOH
139
6
HOH
HOH
263
A
HOH
140
6
HOH
HOH
264
A
HOH
141
6
HOH
HOH
265
A
HOH
142
6
HOH
HOH
266
A
HOH
144
6
HOH
HOH
267
A
HOH
146
6
HOH
HOH
268
A
HOH
151
6
HOH
HOH
269
A
HOH
153
6
HOH
HOH
270
A
HOH
154
6
HOH
HOH
271
A
HOH
155
6
HOH
HOH
272
A
HOH
158
6
HOH
HOH
273
A
HOH
159
6
HOH
HOH
274
A
HOH
160
6
HOH
HOH
275
A
HOH
164
6
HOH
HOH
276
A
HOH
166
6
HOH
HOH
277
A
HOH
168
6
HOH
HOH
278
A
HOH
169
6
HOH
HOH
279
A
HOH
5
6
HOH
HOH
201
B
HOH
6
6
HOH
HOH
202
B
HOH
7
6
HOH
HOH
203
B
HOH
8
6
HOH
HOH
204
B
HOH
9
6
HOH
HOH
205
B
HOH
14
6
HOH
HOH
206
B
HOH
15
6
HOH
HOH
207
B
HOH
20
6
HOH
HOH
208
B
HOH
25
6
HOH
HOH
209
B
HOH
26
6
HOH
HOH
210
B
HOH
27
6
HOH
HOH
211
B
HOH
28
6
HOH
HOH
212
B
HOH
29
6
HOH
HOH
213
B
HOH
32
6
HOH
HOH
214
B
HOH
34
6
HOH
HOH
215
B
HOH
37
6
HOH
HOH
216
B
HOH
39
6
HOH
HOH
217
B
HOH
44
6
HOH
HOH
218
B
HOH
47
6
HOH
HOH
219
B
HOH
49
6
HOH
HOH
220
B
HOH
50
6
HOH
HOH
221
B
HOH
53
6
HOH
HOH
222
B
HOH
54
6
HOH
HOH
223
B
HOH
56
6
HOH
HOH
224
B
HOH
57
6
HOH
HOH
225
B
HOH
59
6
HOH
HOH
226
B
HOH
60
6
HOH
HOH
227
B
HOH
64
6
HOH
HOH
228
B
HOH
66
6
HOH
HOH
229
B
HOH
69
6
HOH
HOH
230
B
HOH
70
6
HOH
HOH
231
B
HOH
72
6
HOH
HOH
232
B
HOH
73
6
HOH
HOH
233
B
HOH
78
6
HOH
HOH
234
B
HOH
80
6
HOH
HOH
235
B
HOH
84
6
HOH
HOH
236
B
HOH
85
6
HOH
HOH
237
B
HOH
86
6
HOH
HOH
238
B
HOH
87
6
HOH
HOH
239
B
HOH
88
6
HOH
HOH
240
B
HOH
89
6
HOH
HOH
241
B
HOH
91
6
HOH
HOH
242
B
HOH
92
6
HOH
HOH
243
B
HOH
94
6
HOH
HOH
244
B
HOH
99
6
HOH
HOH
245
B
HOH
100
6
HOH
HOH
246
B
HOH
101
6
HOH
HOH
247
B
HOH
103
6
HOH
HOH
248
B
HOH
105
6
HOH
HOH
249
B
HOH
106
6
HOH
HOH
250
B
HOH
107
6
HOH
HOH
251
B
HOH
110
6
HOH
HOH
252
B
HOH
112
6
HOH
HOH
253
B
HOH
113
6
HOH
HOH
254
B
HOH
114
6
HOH
HOH
255
B
HOH
115
6
HOH
HOH
256
B
HOH
117
6
HOH
HOH
257
B
HOH
118
6
HOH
HOH
258
B
HOH
122
6
HOH
HOH
259
B
HOH
124
6
HOH
HOH
260
B
HOH
126
6
HOH
HOH
261
B
HOH
127
6
HOH
HOH
262
B
HOH
128
6
HOH
HOH
263
B
HOH
130
6
HOH
HOH
264
B
HOH
132
6
HOH
HOH
265
B
HOH
133
6
HOH
HOH
266
B
HOH
137
6
HOH
HOH
267
B
HOH
143
6
HOH
HOH
268
B
HOH
145
6
HOH
HOH
269
B
HOH
147
6
HOH
HOH
270
B
HOH
148
6
HOH
HOH
271
B
HOH
149
6
HOH
HOH
272
B
HOH
150
6
HOH
HOH
273
B
HOH
156
6
HOH
HOH
274
B
HOH
157
6
HOH
HOH
275
B
HOH
161
6
HOH
HOH
276
B
HOH
162
6
HOH
HOH
277
B
HOH
163
6
HOH
HOH
278
B
HOH
165
6
HOH
HOH
279
B
HOH
167
6
HOH
HOH
280
B
HOH
170
6
HOH
HOH
281
B
HOH
65
6
HOH
HOH
101
C
HOH
95
6
HOH
HOH
102
C
HOH
36
6
HOH
HOH
103
C
HOH
52
6
HOH
HOH
104
C
HOH
152
6
HOH
HOH
105
C
47.980
1.800
1.800
21.900
21.900
Phaser MODE: MR_AUTO
PRO
1
n
1
PRO
1
A
GLN
2
n
2
GLN
2
A
ILE
3
n
3
ILE
3
A
THR
4
n
4
THR
4
A
LEU
5
n
5
LEU
5
A
TRP
6
n
6
TRP
6
A
LYS
7
n
7
LYS
7
A
ARG
8
n
8
ARG
8
A
PRO
9
n
9
PRO
9
A
LEU
10
n
10
LEU
10
A
VAL
11
n
11
VAL
11
A
THR
12
n
12
THR
12
A
ILE
13
n
13
ILE
13
A
LYS
14
n
14
LYS
14
A
ILE
15
n
15
ILE
15
A
GLY
16
n
16
GLY
16
A
GLY
17
n
17
GLY
17
A
GLN
18
n
18
GLN
18
A
LEU
19
n
19
LEU
19
A
LYS
20
n
20
LYS
20
A
GLU
21
n
21
GLU
21
A
ALA
22
n
22
ALA
22
A
LEU
23
n
23
LEU
23
A
LEU
24
n
24
LEU
24
A
ASP
25
n
25
ASP
25
A
THR
26
n
26
THR
26
A
GLY
27
n
27
GLY
27
A
ALA
28
n
28
ALA
28
A
ASP
29
n
29
ASP
29
A
ASP
30
n
30
ASP
30
A
THR
31
n
31
THR
31
A
VAL
32
n
32
VAL
32
A
LEU
33
n
33
LEU
33
A
GLU
34
n
34
GLU
34
A
GLU
35
n
35
GLU
35
A
MET
36
n
36
MET
36
A
ASN
37
n
37
ASN
37
A
LEU
38
n
38
LEU
38
A
PRO
39
n
39
PRO
39
A
GLY
40
n
40
GLY
40
A
ARG
41
n
41
ARG
41
A
TRP
42
n
42
TRP
42
A
LYS
43
n
43
LYS
43
A
PRO
44
n
44
PRO
44
A
LYS
45
n
45
LYS
45
A
MET
46
n
46
MET
46
A
ILE
47
n
47
ILE
47
A
GLY
48
n
48
GLY
48
A
GLY
49
n
49
GLY
49
A
ILE
50
n
50
ILE
50
A
GLY
51
n
51
GLY
51
A
GLY
52
n
52
GLY
52
A
PHE
53
n
53
PHE
53
A
ILE
54
n
54
ILE
54
A
LYS
55
n
55
LYS
55
A
VAL
56
n
56
VAL
56
A
ARG
57
n
57
ARG
57
A
GLN
58
n
58
GLN
58
A
TYR
59
n
59
TYR
59
A
ASP
60
n
60
ASP
60
A
GLN
61
n
61
GLN
61
A
ILE
62
n
62
ILE
62
A
LEU
63
n
63
LEU
63
A
ILE
64
n
64
ILE
64
A
GLU
65
n
65
GLU
65
A
ILE
66
n
66
ILE
66
A
CYS
67
n
67
CYS
67
A
GLY
68
n
68
GLY
68
A
HIS
69
n
69
HIS
69
A
LYS
70
n
70
LYS
70
A
ALA
71
n
71
ALA
71
A
ILE
72
n
72
ILE
72
A
GLY
73
n
73
GLY
73
A
THR
74
n
74
THR
74
A
VAL
75
n
75
VAL
75
A
LEU
76
n
76
LEU
76
A
VAL
77
n
77
VAL
77
A
GLY
78
n
78
GLY
78
A
PRO
79
n
79
PRO
79
A
THR
80
n
80
THR
80
A
PRO
81
n
81
PRO
81
A
VAL
82
n
82
VAL
82
A
ASN
83
n
83
ASN
83
A
ILE
84
n
84
ILE
84
A
ILE
85
n
85
ILE
85
A
GLY
86
n
86
GLY
86
A
ARG
87
n
87
ARG
87
A
ASN
88
n
88
ASN
88
A
LEU
89
n
89
LEU
89
A
LEU
90
n
90
LEU
90
A
THR
91
n
91
THR
91
A
GLN
92
n
92
GLN
92
A
ILE
93
n
93
ILE
93
A
GLY
94
n
94
GLY
94
A
CYS
95
n
95
CYS
95
A
THR
96
n
96
THR
96
A
LEU
97
n
97
LEU
97
A
ASN
98
n
98
ASN
98
A
PHE
99
n
99
PHE
99
A
PRO
1
n
1
PRO
1
B
GLN
2
n
2
GLN
2
B
ILE
3
n
3
ILE
3
B
THR
4
n
4
THR
4
B
LEU
5
n
5
LEU
5
B
TRP
6
n
6
TRP
6
B
LYS
7
n
7
LYS
7
B
ARG
8
n
8
ARG
8
B
PRO
9
n
9
PRO
9
B
LEU
10
n
10
LEU
10
B
VAL
11
n
11
VAL
11
B
THR
12
n
12
THR
12
B
ILE
13
n
13
ILE
13
B
LYS
14
n
14
LYS
14
B
ILE
15
n
15
ILE
15
B
GLY
16
n
16
GLY
16
B
GLY
17
n
17
GLY
17
B
GLN
18
n
18
GLN
18
B
LEU
19
n
19
LEU
19
B
LYS
20
n
20
LYS
20
B
GLU
21
n
21
GLU
21
B
ALA
22
n
22
ALA
22
B
LEU
23
n
23
LEU
23
B
LEU
24
n
24
LEU
24
B
ASP
25
n
25
ASP
25
B
THR
26
n
26
THR
26
B
GLY
27
n
27
GLY
27
B
ALA
28
n
28
ALA
28
B
ASP
29
n
29
ASP
29
B
ASP
30
n
30
ASP
30
B
THR
31
n
31
THR
31
B
VAL
32
n
32
VAL
32
B
LEU
33
n
33
LEU
33
B
GLU
34
n
34
GLU
34
B
GLU
35
n
35
GLU
35
B
MET
36
n
36
MET
36
B
ASN
37
n
37
ASN
37
B
LEU
38
n
38
LEU
38
B
PRO
39
n
39
PRO
39
B
GLY
40
n
40
GLY
40
B
ARG
41
n
41
ARG
41
B
TRP
42
n
42
TRP
42
B
LYS
43
n
43
LYS
43
B
PRO
44
n
44
PRO
44
B
LYS
45
n
45
LYS
45
B
MET
46
n
46
MET
46
B
ILE
47
n
47
ILE
47
B
GLY
48
n
48
GLY
48
B
GLY
49
n
49
GLY
49
B
ILE
50
n
50
ILE
50
B
GLY
51
n
51
GLY
51
B
GLY
52
n
52
GLY
52
B
PHE
53
n
53
PHE
53
B
ILE
54
n
54
ILE
54
B
LYS
55
n
55
LYS
55
B
VAL
56
n
56
VAL
56
B
ARG
57
n
57
ARG
57
B
GLN
58
n
58
GLN
58
B
TYR
59
n
59
TYR
59
B
ASP
60
n
60
ASP
60
B
GLN
61
n
61
GLN
61
B
ILE
62
n
62
ILE
62
B
LEU
63
n
63
LEU
63
B
ILE
64
n
64
ILE
64
B
GLU
65
n
65
GLU
65
B
ILE
66
n
66
ILE
66
B
CYS
67
n
67
CYS
67
B
GLY
68
n
68
GLY
68
B
HIS
69
n
69
HIS
69
B
LYS
70
n
70
LYS
70
B
ALA
71
n
71
ALA
71
B
ILE
72
n
72
ILE
72
B
GLY
73
n
73
GLY
73
B
THR
74
n
74
THR
74
B
VAL
75
n
75
VAL
75
B
LEU
76
n
76
LEU
76
B
VAL
77
n
77
VAL
77
B
GLY
78
n
78
GLY
78
B
PRO
79
n
79
PRO
79
B
THR
80
n
80
THR
80
B
PRO
81
n
81
PRO
81
B
VAL
82
n
82
VAL
82
B
ASN
83
n
83
ASN
83
B
ILE
84
n
84
ILE
84
B
ILE
85
n
85
ILE
85
B
GLY
86
n
86
GLY
86
B
ARG
87
n
87
ARG
87
B
ASN
88
n
88
ASN
88
B
LEU
89
n
89
LEU
89
B
LEU
90
n
90
LEU
90
B
THR
91
n
91
THR
91
B
GLN
92
n
92
GLN
92
B
ILE
93
n
93
ILE
93
B
GLY
94
n
94
GLY
94
B
CYS
95
n
95
CYS
95
B
THR
96
n
96
THR
96
B
LEU
97
n
97
LEU
97
B
ASN
98
n
98
ASN
98
B
PHE
99
n
99
PHE
99
B
IVA
1
n
1
IVA
1
C
VAL
2
n
2
VAL
2
C
VAL
3
n
3
VAL
3
C
STA
4
n
4
STA
4
C
ALA
5
n
5
ALA
5
C
STA
6
n
6
STA
6
C
author_and_software_defined_assembly
PISA
3
trimeric
5850
-40
9510
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
N
ILE
3
A
N
ILE
3
B
O
LEU
97
B
O
LEU
97
B
O
ASN
98
B
O
ASN
98
A
N
THR
96
A
N
THR
96
A
N
LEU
97
A
N
LEU
97
B
O
ILE
3
B
O
ILE
3
C
O
VAL
3
C
O
VAL
3
A
N
GLY
48
A
N
GLY
48
A
N
LYS
43
A
N
LYS
43
A
O
GLN
58
A
O
GLN
58
A
N
ILE
64
A
N
ILE
64
A
O
ALA
71
A
O
ALA
71
A
O
LEU
76
A
O
LEU
76
A
N
LEU
33
A
N
LEU
33
A
N
VAL
32
A
N
VAL
32
A
O
ILE
84
A
O
ILE
84
A
O
ILE
85
A
O
ILE
85
A
N
LEU
23
A
N
LEU
23
A
O
LYS
20
A
O
LYS
20
A
N
ILE
13
A
N
ILE
13
A
N
LYS
14
A
N
LYS
14
A
O
GLU
65
A
O
GLU
65
B
N
LYS
43
B
N
LYS
43
B
O
GLN
58
B
O
GLN
58
B
N
ARG
57
B
N
ARG
57
B
O
VAL
77
B
O
VAL
77
B
O
LEU
76
B
O
LEU
76
B
N
LEU
33
B
N
LEU
33
B
N
VAL
32
B
N
VAL
32
B
O
ILE
84
B
O
ILE
84
B
O
ILE
85
B
O
ILE
85
B
N
LEU
23
B
N
LEU
23
B
O
LYS
20
B
O
LYS
20
B
N
ILE
13
B
N
ILE
13
B
N
LYS
14
B
N
LYS
14
B
O
GLU
65
B
O
GLU
65
1
A
CG
GLU
35
A
CG
GLU
35
1
Y
1
A
CD
GLU
35
A
CD
GLU
35
1
Y
1
A
OE1
GLU
35
A
OE1
GLU
35
1
Y
1
A
OE2
GLU
35
A
OE2
GLU
35
1
Y
1
B
NZ
LYS
20
B
NZ
LYS
20
1
Y
1
B
NZ
LYS
70
B
NZ
LYS
70
1
Y
1
A
A
O
O
HOH
HOH
254
258
1.86
1
B
B
O
NE2
ILE
GLN
72
92
2.12
A
1
C
STA
4
33.57
1
C
C
STA
ALA
4
5
-112.74
1
A
ASP
30
0.070
SIDE CHAIN
1
A
GLN
92
0.097
SIDE CHAIN
1
C
C
C
N
ALA
STA
5
6
1.18
1
12.19
1.60
110.90
123.09
A
A
A
CG1
CB
CG2
VAL
VAL
VAL
32
32
32
A
A
N
1
25.62
2.20
117.20
142.82
C
C
C
CA
C
N
STA
STA
ALA
4
4
5
Y
1
C
C
C
N
ALA
STA
5
6
-0.157
0.023
1.336
1.179
Y
1
B
B
CE
O
MET
THR
46
80
2.12
C
1_555
4_455
1
A
GLU
35
-35.55
124.23
95.580
14.7297
4.790
-0.0200
0.0000
-0.0000
-0.0100
0.0000
0.0200
0.9670
0.9540
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
U VALUES : REFINED INDIVIDUALLY
0.1762
0.1459
0.1475
1.103
18.96
3543
70371
5.0
97.77
0.1778
0.1467
1.000
0.160
0.9194
0.9340
0.0210
0.0319
0.0333
RANDOM
1
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
0.0320
0.0330
0.8000
0.8000
1.2000
MAXIMUM LIKELIHOOD
MASK
1.103
18.96
165
1757
30
0
1562
0.010
0.019
1728
0.000
0.020
1194
1.442
2.017
2332
2.064
3.000
2972
6.865
5.000
215
40.956
24.516
62
14.202
15.000
329
11.903
15.000
11
0.139
0.200
276
0.015
0.021
1834
0.002
0.020
304
10.330
3.000
2915
35.424
5.000
66
10.978
5.000
2987
0.2780
0.2620
1.132
216
4652
4868
20
99.49
1.103
92.930
4EJD
70609
70609
0.089
1
8.3
3.4
98.3
0.483
1.103
1.160
1.5
34370
10342
0.483
1
3.3
99.9
0.335
1.160
1.230
2.2
33166
9802
0.335
1
3.4
99.9
0.262
1.230
1.320
2.8
31661
9277
0.262
1
3.4
99.9
0.194
1.320
1.420
3.8
29480
8587
0.194
1
3.4
99.8
0.127
1.420
1.560
5.6
27331
7945
0.127
1
3.4
99.9
0.079
1.560
1.740
8.9
24667
7235
0.079
1
3.4
99.8
0.068
1.740
2.010
8.1
21652
6378
0.068
1
3.4
99.6
0.077
2.010
2.470
7.8
17123
5428
0.077
1
3.2
99.1
0.043
2.470
3.490
14.2
14361
4155
0.043
1
3.5
96.6
0.052
3.490
21.901
10.8
4093
1460
0.052
1
2.8
57.9
data reduction
Andrew G.W. Leslie
andrew@mrc-lmb.cam.ac.uk
2010/01/06
http://www.mrc-lmb.cam.ac.uk/harry/mosflm/
MOSFLM
package
3.3.16
data scaling
Phil R. Evans
pre@mrc-lmb.cam.ac.uk
2010/01/06
Fortran_77
http://www.ccp4.ac.uk/dist/html/scala.html
SCALA
other
3.3.16
phasing
Randy J. Read
cimr-phaser@lists.cam.ac.uk
Mon Feb 8 16:31:08 2010
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
2.1.4
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
data extraction
PDB
deposit@deposit.rcsb.org
April 22, 2011
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.11
data collection
Blu-Ice
Protease (E.C.3.4.23.16), pepstatin
HIV Protease (PR) dimer in closed form with pepstatin in active site and fragment 1F1 in the outside/top of flap
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
3
N
N
3
N
N
6
N
N
6
N
N
6
N
N
A
GLY
86
A
GLY
86
HELX_P
A
THR
91
A
THR
91
1
1
6
A
GLN
92
A
GLN
92
HELX_P
A
GLY
94
A
GLY
94
5
2
3
B
GLY
86
B
GLY
86
HELX_P
B
THR
91
B
THR
91
1
3
6
B
GLN
92
B
GLN
92
HELX_P
B
GLY
94
B
GLY
94
5
4
3
covale
1.339
sing
C
IVA
1
C
C
IVA
1
1_555
C
VAL
2
C
N
VAL
2
1_555
covale
1.416
sing
C
VAL
3
C
C
VAL
3
1_555
C
STA
4
C
N
STA
4
1_555
covale
1.317
sing
C
STA
4
C
C
STA
4
1_555
C
ALA
5
C
N
ALA
5
1_555
covale
1.179
sing
C
ALA
5
C
C
ALA
5
1_555
C
STA
6
C
N
STA
6
1_555
HYDROLASE/HYDROLASE INHIBITOR
apo protease, allostery, fragment binding, HYDROLASE-HYDROLASE INHIBITOR complex
POL_HV1Z2
UNP
1
490
P12499
PQITLWQRPLVTIKIGGQLKEALLDTGADDTVLEEMNLPGKWKPKMIGGIGGFIKVRQYDQILIEICGHKAIGTVLVGPT
PVNIIGRNLLTQIGCTLNF
4EJD
PDB
2
1
4EJD
(IVA)VV(STA)A(STA)
490
588
4EJD
1
99
P12499
A
1
1
99
490
588
4EJD
1
99
P12499
B
1
1
99
1
6
4EJD
1
6
4EJD
C
2
1
6
1
GLN
CONFLICT
LYS
7
4EJD
A
P12499
UNP
496
7
1
LYS
CONFLICT
ARG
41
4EJD
A
P12499
UNP
530
41
2
GLN
CONFLICT
LYS
7
4EJD
B
P12499
UNP
496
7
2
LYS
CONFLICT
ARG
41
4EJD
B
P12499
UNP
530
41
4
9
8
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
GLN
2
A
GLN
2
A
ILE
3
A
ILE
3
B
THR
96
B
THR
96
B
ASN
98
B
ASN
98
A
THR
96
A
THR
96
A
ASN
98
A
ASN
98
B
GLN
2
B
GLN
2
B
ILE
3
B
ILE
3
C
VAL
2
C
VAL
2
C
VAL
3
C
VAL
3
A
LYS
43
A
LYS
43
A
GLY
49
A
GLY
49
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
A
HIS
69
A
HIS
69
A
VAL
77
A
VAL
77
A
VAL
32
A
VAL
32
A
LEU
33
A
LEU
33
A
ILE
84
A
ILE
84
A
ILE
85
A
ILE
85
A
GLN
18
A
GLN
18
A
LEU
24
A
LEU
24
A
LEU
10
A
LEU
10
A
ILE
15
A
ILE
15
A
GLY
52
A
GLY
52
A
ILE
66
A
ILE
66
B
LYS
43
B
LYS
43
B
GLY
49
B
GLY
49
B
GLY
52
B
GLY
52
B
ILE
66
B
ILE
66
B
HIS
69
B
HIS
69
B
VAL
77
B
VAL
77
B
VAL
32
B
VAL
32
B
LEU
33
B
LEU
33
B
ILE
84
B
ILE
84
B
ILE
85
B
ILE
85
B
GLN
18
B
GLN
18
B
LEU
24
B
LEU
24
B
LEU
10
B
LEU
10
B
ILE
15
B
ILE
15
B
GLY
52
B
GLY
52
B
ILE
66
B
ILE
66
BINDING SITE FOR RESIDUE BME A 101
Software
7
BINDING SITE FOR RESIDUE 1F1 A 102
Software
11
BINDING SITE FOR RESIDUE GOL B 101
Software
10
BINDING SITE FOR RESIDUE BME B 102
Software
5
BINDING SITE FOR RESIDUE BME B 103
Software
5
BINDING SITE FOR CHAIN C OF PEPSTATIN
Software
22
A
LEU
10
A
LEU
10
7
1_555
A
VAL
11
A
VAL
11
7
1_555
A
THR
12
A
THR
12
7
1_555
A
CYS
67
A
CYS
67
7
1_555
A
HOH
207
I
HOH
7
1_555
B
LYS
7
B
LYS
7
7
1_455
B
HOH
246
J
HOH
7
1_455
A
PRO
44
A
PRO
44
11
1_555
A
LYS
45
A
LYS
45
11
1_555
A
LYS
55
A
LYS
55
11
1_555
A
VAL
56
A
VAL
56
11
1_555
A
ARG
57
A
ARG
57
11
1_555
A
THR
91
A
THR
91
11
3_655
A
GLN
92
A
GLN
92
11
3_655
A
GLY
94
A
GLY
94
11
3_655
A
HOH
209
I
HOH
11
3_655
A
HOH
278
I
HOH
11
1_555
B
HOH
233
J
HOH
11
3_655
A
GLY
49
A
GLY
49
10
4_455
A
GLY
51
A
GLY
51
10
4_455
A
GLY
52
A
GLY
52
10
4_455
B
PRO
44
B
PRO
44
10
1_555
B
MET
46
B
MET
46
10
1_555
B
LYS
55
B
LYS
55
10
1_555
B
PRO
81
B
PRO
81
10
4_455
B
HOH
225
J
HOH
10
1_555
B
HOH
251
J
HOH
10
4_455
C
HOH
104
K
HOH
10
4_455
A
LYS
7
A
LYS
7
5
1_655
A
HOH
227
I
HOH
5
1_655
B
VAL
11
B
VAL
11
5
1_555
B
CYS
67
B
CYS
67
5
1_555
B
BME
103
H
BME
5
1_555
A
LYS
7
A
LYS
7
5
1_655
A
HOH
227
I
HOH
5
1_655
B
THR
12
B
THR
12
5
1_555
B
CYS
67
B
CYS
67
5
1_555
B
BME
102
G
BME
5
1_555
A
ARG
8
A
ARG
8
22
1_555
A
ASP
25
A
ASP
25
22
1_555
A
GLY
27
A
GLY
27
22
1_555
A
ALA
28
A
ALA
28
22
1_555
A
ASP
29
A
ASP
29
22
1_555
A
ASP
30
A
ASP
30
22
1_555
A
LYS
45
A
LYS
45
22
1_555
A
ILE
47
A
ILE
47
22
1_555
A
GLY
48
A
GLY
48
22
1_555
A
GLY
49
A
GLY
49
22
1_555
A
ILE
84
A
ILE
84
22
1_555
B
ARG
8
B
ARG
8
22
1_555
B
ASP
25
B
ASP
25
22
1_555
B
GLY
27
B
GLY
27
22
1_555
B
ALA
28
B
ALA
28
22
1_555
B
ASP
29
B
ASP
29
22
1_555
B
ASP
30
B
ASP
30
22
1_555
B
GLY
48
B
GLY
48
22
1_555
B
HOH
231
J
HOH
22
1_555
C
HOH
102
K
HOH
22
1_555
C
HOH
103
K
HOH
22
1_555
C
HOH
105
K
HOH
22
1_555
19
P 21 21 21