0.022092
0.000000
0.007768
0.000000
0.013702
0.000000
0.000000
0.000000
0.020106
0.000000
0.000000
0.000000
Schiebel, J.
Heine, A.
Klebe, G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
2
90.000
109.370
90.000
45.265
72.980
52.721
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
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
UK
Structure
STRUE6
2005
1878-4186
24
1398
1409
10.1016/j.str.2016.06.010
27452405
High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits.
2016
10.2210/pdb5p69/pdb
pdb_00005p69
100
1
CCD
2014-02-15
MAR CCD 165 mm
SINGLE WAVELENGTH
M
x-ray
1
0.8944
1.0
14.3
BESSY
0.8944
SYNCHROTRON
BESSY BEAMLINE 14.3
33813.855
endothiapepsin
3.4.23.22
1
nat
polymer
18.015
water
165
nat
water
no
no
STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASEVDGQTIYTPSKSTTAKLLSGATWSISYG
DGSSSSGDVYTDTVSVGGLTVTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKASLDSPVFTAD
LGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTSTGYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVS
GAKSSSSVGGYVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGIGINIFGDVALKAAFVVFNGA
TTPTLGFASK
STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASEVDGQTIYTPSKSTTAKLLSGATWSISYG
DGSSSSGDVYTDTVSVGGLTVTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKASLDSPVFTAD
LGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTSTGYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVS
GAKSSSSVGGYVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGIGINIFGDVALKAAFVVFNGA
TTPTLGFASK
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
5116
Cryphonectria parasitica
1
2.43
49.37
VAPOR DIFFUSION, SITTING DROP
4.6
0.1 M ammonium acetate, 0.1 M sodium acetate, 24-30% PEG 4000; crystal obtained by streak-seeding and soaked with 90 mM of fragment 270 with the SMILES code CC(C)(C)C(=O)N1CCC(CC1)C(=O)NC1CC1
290
pdbx_deposit_group
database_2
pdbx_deposit_group
repository
Initial release
Database references
Database references
Structure summary
Database references
Structure summary
1
0
2016-08-03
1
1
2016-08-10
1
2
2017-01-11
1
3
2018-02-21
1
4
2021-11-17
_pdbx_deposit_group.group_type
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_deposit_group.group_description
RCSB
Y
RCSB
2016-06-28
REL
REL
High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits.
High-Throughput Crystallography: Reliable and Efficient Identification of Fragment Hits.
undefined
HOH
water
HOH
166
2
HOH
HOH
401
A
HOH
126
2
HOH
HOH
402
A
HOH
40
2
HOH
HOH
403
A
HOH
117
2
HOH
HOH
404
A
HOH
21
2
HOH
HOH
405
A
HOH
145
2
HOH
HOH
406
A
HOH
68
2
HOH
HOH
407
A
HOH
131
2
HOH
HOH
408
A
HOH
44
2
HOH
HOH
409
A
HOH
97
2
HOH
HOH
410
A
HOH
66
2
HOH
HOH
411
A
HOH
122
2
HOH
HOH
412
A
HOH
118
2
HOH
HOH
413
A
HOH
14
2
HOH
HOH
414
A
HOH
144
2
HOH
HOH
415
A
HOH
124
2
HOH
HOH
416
A
HOH
10
2
HOH
HOH
417
A
HOH
1
2
HOH
HOH
418
A
HOH
82
2
HOH
HOH
419
A
HOH
28
2
HOH
HOH
420
A
HOH
24
2
HOH
HOH
421
A
HOH
147
2
HOH
HOH
422
A
HOH
67
2
HOH
HOH
423
A
HOH
54
2
HOH
HOH
424
A
HOH
148
2
HOH
HOH
425
A
HOH
146
2
HOH
HOH
426
A
HOH
79
2
HOH
HOH
427
A
HOH
111
2
HOH
HOH
428
A
HOH
58
2
HOH
HOH
429
A
HOH
119
2
HOH
HOH
430
A
HOH
80
2
HOH
HOH
431
A
HOH
91
2
HOH
HOH
432
A
HOH
2
2
HOH
HOH
433
A
HOH
31
2
HOH
HOH
434
A
HOH
13
2
HOH
HOH
435
A
HOH
34
2
HOH
HOH
436
A
HOH
26
2
HOH
HOH
437
A
HOH
123
2
HOH
HOH
438
A
HOH
41
2
HOH
HOH
439
A
HOH
23
2
HOH
HOH
440
A
HOH
154
2
HOH
HOH
441
A
HOH
81
2
HOH
HOH
442
A
HOH
4
2
HOH
HOH
443
A
HOH
78
2
HOH
HOH
444
A
HOH
121
2
HOH
HOH
445
A
HOH
76
2
HOH
HOH
446
A
HOH
94
2
HOH
HOH
447
A
HOH
103
2
HOH
HOH
448
A
HOH
29
2
HOH
HOH
449
A
HOH
114
2
HOH
HOH
450
A
HOH
33
2
HOH
HOH
451
A
HOH
75
2
HOH
HOH
452
A
HOH
90
2
HOH
HOH
453
A
HOH
5
2
HOH
HOH
454
A
HOH
51
2
HOH
HOH
455
A
HOH
20
2
HOH
HOH
456
A
HOH
35
2
HOH
HOH
457
A
HOH
176
2
HOH
HOH
458
A
HOH
50
2
HOH
HOH
459
A
HOH
52
2
HOH
HOH
460
A
HOH
8
2
HOH
HOH
461
A
HOH
3
2
HOH
HOH
462
A
HOH
30
2
HOH
HOH
463
A
HOH
43
2
HOH
HOH
464
A
HOH
11
2
HOH
HOH
465
A
HOH
133
2
HOH
HOH
466
A
HOH
46
2
HOH
HOH
467
A
HOH
18
2
HOH
HOH
468
A
HOH
74
2
HOH
HOH
469
A
HOH
16
2
HOH
HOH
470
A
HOH
134
2
HOH
HOH
471
A
HOH
45
2
HOH
HOH
472
A
HOH
98
2
HOH
HOH
473
A
HOH
12
2
HOH
HOH
474
A
HOH
38
2
HOH
HOH
475
A
HOH
7
2
HOH
HOH
476
A
HOH
25
2
HOH
HOH
477
A
HOH
174
2
HOH
HOH
478
A
HOH
85
2
HOH
HOH
479
A
HOH
62
2
HOH
HOH
480
A
HOH
143
2
HOH
HOH
481
A
HOH
158
2
HOH
HOH
482
A
HOH
157
2
HOH
HOH
483
A
HOH
151
2
HOH
HOH
484
A
HOH
37
2
HOH
HOH
485
A
HOH
19
2
HOH
HOH
486
A
HOH
47
2
HOH
HOH
487
A
HOH
136
2
HOH
HOH
488
A
HOH
178
2
HOH
HOH
489
A
HOH
105
2
HOH
HOH
490
A
HOH
89
2
HOH
HOH
491
A
HOH
72
2
HOH
HOH
492
A
HOH
159
2
HOH
HOH
493
A
HOH
132
2
HOH
HOH
494
A
HOH
150
2
HOH
HOH
495
A
HOH
55
2
HOH
HOH
496
A
HOH
71
2
HOH
HOH
497
A
HOH
64
2
HOH
HOH
498
A
HOH
15
2
HOH
HOH
499
A
HOH
32
2
HOH
HOH
500
A
HOH
92
2
HOH
HOH
501
A
HOH
152
2
HOH
HOH
502
A
HOH
42
2
HOH
HOH
503
A
HOH
108
2
HOH
HOH
504
A
HOH
53
2
HOH
HOH
505
A
HOH
155
2
HOH
HOH
506
A
HOH
61
2
HOH
HOH
507
A
HOH
84
2
HOH
HOH
508
A
HOH
39
2
HOH
HOH
509
A
HOH
125
2
HOH
HOH
510
A
HOH
59
2
HOH
HOH
511
A
HOH
36
2
HOH
HOH
512
A
HOH
17
2
HOH
HOH
513
A
HOH
170
2
HOH
HOH
514
A
HOH
96
2
HOH
HOH
515
A
HOH
88
2
HOH
HOH
516
A
HOH
100
2
HOH
HOH
517
A
HOH
127
2
HOH
HOH
518
A
HOH
165
2
HOH
HOH
519
A
HOH
128
2
HOH
HOH
520
A
HOH
112
2
HOH
HOH
521
A
HOH
56
2
HOH
HOH
522
A
HOH
130
2
HOH
HOH
523
A
HOH
171
2
HOH
HOH
524
A
HOH
57
2
HOH
HOH
525
A
HOH
22
2
HOH
HOH
526
A
HOH
73
2
HOH
HOH
527
A
HOH
138
2
HOH
HOH
528
A
HOH
106
2
HOH
HOH
529
A
HOH
77
2
HOH
HOH
530
A
HOH
49
2
HOH
HOH
531
A
HOH
107
2
HOH
HOH
532
A
HOH
95
2
HOH
HOH
533
A
HOH
101
2
HOH
HOH
534
A
HOH
172
2
HOH
HOH
535
A
HOH
153
2
HOH
HOH
536
A
HOH
48
2
HOH
HOH
537
A
HOH
27
2
HOH
HOH
538
A
HOH
135
2
HOH
HOH
539
A
HOH
141
2
HOH
HOH
540
A
HOH
142
2
HOH
HOH
541
A
HOH
63
2
HOH
HOH
542
A
HOH
139
2
HOH
HOH
543
A
HOH
93
2
HOH
HOH
544
A
HOH
156
2
HOH
HOH
545
A
HOH
168
2
HOH
HOH
546
A
HOH
83
2
HOH
HOH
547
A
HOH
9
2
HOH
HOH
548
A
HOH
113
2
HOH
HOH
549
A
HOH
140
2
HOH
HOH
550
A
HOH
115
2
HOH
HOH
551
A
HOH
177
2
HOH
HOH
552
A
HOH
149
2
HOH
HOH
553
A
HOH
129
2
HOH
HOH
554
A
HOH
179
2
HOH
HOH
555
A
HOH
116
2
HOH
HOH
556
A
HOH
87
2
HOH
HOH
557
A
HOH
109
2
HOH
HOH
558
A
HOH
120
2
HOH
HOH
559
A
HOH
110
2
HOH
HOH
560
A
HOH
70
2
HOH
HOH
561
A
HOH
160
2
HOH
HOH
562
A
HOH
137
2
HOH
HOH
563
A
HOH
175
2
HOH
HOH
564
A
HOH
161
2
HOH
HOH
565
A
4.000
36.860
Phaser MODE: MR_AUTO
SER
1
n
1
SER
1
A
THR
2
n
2
THR
2
A
GLY
3
n
3
GLY
3
A
SER
4
n
4
SER
4
A
ALA
5
n
5
ALA
5
A
THR
6
n
6
THR
6
A
THR
7
n
7
THR
7
A
THR
8
n
8
THR
8
A
PRO
9
n
9
PRO
9
A
ILE
10
n
10
ILE
10
A
ASP
11
n
11
ASP
11
A
SER
12
n
12
SER
12
A
LEU
13
n
13
LEU
13
A
ASP
14
n
14
ASP
14
A
ASP
15
n
15
ASP
15
A
ALA
16
n
16
ALA
16
A
TYR
17
n
17
TYR
17
A
ILE
18
n
18
ILE
18
A
THR
19
n
19
THR
19
A
PRO
20
n
20
PRO
20
A
VAL
21
n
21
VAL
21
A
GLN
22
n
22
GLN
22
A
ILE
23
n
23
ILE
23
A
GLY
24
n
24
GLY
24
A
THR
25
n
25
THR
25
A
PRO
26
n
26
PRO
26
A
ALA
27
n
27
ALA
27
A
GLN
28
n
28
GLN
28
A
THR
29
n
29
THR
29
A
LEU
30
n
30
LEU
30
A
ASN
31
n
31
ASN
31
A
LEU
32
n
32
LEU
32
A
ASP
33
n
33
ASP
33
A
PHE
34
n
34
PHE
34
A
ASP
35
n
35
ASP
35
A
THR
36
n
36
THR
36
A
GLY
37
n
37
GLY
37
A
SER
38
n
38
SER
38
A
SER
39
n
39
SER
39
A
ASP
40
n
40
ASP
40
A
LEU
41
n
41
LEU
41
A
TRP
42
n
42
TRP
42
A
VAL
43
n
43
VAL
43
A
PHE
44
n
44
PHE
44
A
SER
45
n
45
SER
45
A
SER
46
n
46
SER
46
A
GLU
47
n
47
GLU
47
A
THR
48
n
48
THR
48
A
THR
49
n
49
THR
49
A
ALA
50
n
50
ALA
50
A
SER
51
n
51
SER
51
A
GLU
52
n
52
GLU
52
A
VAL
53
n
53
VAL
53
A
ASP
54
n
54
ASP
54
A
GLY
55
n
55
GLY
55
A
GLN
56
n
56
GLN
56
A
THR
57
n
57
THR
57
A
ILE
58
n
58
ILE
58
A
TYR
59
n
59
TYR
59
A
THR
60
n
60
THR
60
A
PRO
61
n
61
PRO
61
A
SER
62
n
62
SER
62
A
LYS
63
n
63
LYS
63
A
SER
64
n
64
SER
64
A
THR
65
n
65
THR
65
A
THR
66
n
66
THR
66
A
ALA
67
n
67
ALA
67
A
LYS
68
n
68
LYS
68
A
LEU
69
n
69
LEU
69
A
LEU
70
n
70
LEU
70
A
SER
71
n
71
SER
71
A
GLY
72
n
72
GLY
72
A
ALA
73
n
73
ALA
73
A
THR
74
n
74
THR
74
A
TRP
75
n
75
TRP
75
A
SER
76
n
76
SER
76
A
ILE
77
n
77
ILE
77
A
SER
78
n
78
SER
78
A
TYR
79
n
79
TYR
79
A
GLY
80
n
80
GLY
80
A
ASP
81
n
81
ASP
81
A
GLY
82
n
82
GLY
82
A
SER
83
n
83
SER
83
A
SER
84
n
84
SER
84
A
SER
85
n
85
SER
85
A
SER
86
n
86
SER
86
A
GLY
87
n
87
GLY
87
A
ASP
88
n
88
ASP
88
A
VAL
89
n
89
VAL
89
A
TYR
90
n
90
TYR
90
A
THR
91
n
91
THR
91
A
ASP
92
n
92
ASP
92
A
THR
93
n
93
THR
93
A
VAL
94
n
94
VAL
94
A
SER
95
n
95
SER
95
A
VAL
96
n
96
VAL
96
A
GLY
97
n
97
GLY
97
A
GLY
98
n
98
GLY
98
A
LEU
99
n
99
LEU
99
A
THR
100
n
100
THR
100
A
VAL
101
n
101
VAL
101
A
THR
102
n
102
THR
102
A
GLY
103
n
103
GLY
103
A
GLN
104
n
104
GLN
104
A
ALA
105
n
105
ALA
105
A
VAL
106
n
106
VAL
106
A
GLU
107
n
107
GLU
107
A
SER
108
n
108
SER
108
A
ALA
109
n
109
ALA
109
A
LYS
110
n
110
LYS
110
A
LYS
111
n
111
LYS
111
A
VAL
112
n
112
VAL
112
A
SER
113
n
113
SER
113
A
SER
114
n
114
SER
114
A
SER
115
n
115
SER
115
A
PHE
116
n
116
PHE
116
A
THR
117
n
117
THR
117
A
GLU
118
n
118
GLU
118
A
ASP
119
n
119
ASP
119
A
SER
120
n
120
SER
120
A
THR
121
n
121
THR
121
A
ILE
122
n
122
ILE
122
A
ASP
123
n
123
ASP
123
A
GLY
124
n
124
GLY
124
A
LEU
125
n
125
LEU
125
A
LEU
126
n
126
LEU
126
A
GLY
127
n
127
GLY
127
A
LEU
128
n
128
LEU
128
A
ALA
129
n
129
ALA
129
A
PHE
130
n
130
PHE
130
A
SER
131
n
131
SER
131
A
THR
132
n
132
THR
132
A
LEU
133
n
133
LEU
133
A
ASN
134
n
134
ASN
134
A
THR
135
n
135
THR
135
A
VAL
136
n
136
VAL
136
A
SER
137
n
137
SER
137
A
PRO
138
n
138
PRO
138
A
THR
139
n
139
THR
139
A
GLN
140
n
140
GLN
140
A
GLN
141
n
141
GLN
141
A
LYS
142
n
142
LYS
142
A
THR
143
n
143
THR
143
A
PHE
144
n
144
PHE
144
A
PHE
145
n
145
PHE
145
A
ASP
146
n
146
ASP
146
A
ASN
147
n
147
ASN
147
A
ALA
148
n
148
ALA
148
A
LYS
149
n
149
LYS
149
A
ALA
150
n
150
ALA
150
A
SER
151
n
151
SER
151
A
LEU
152
n
152
LEU
152
A
ASP
153
n
153
ASP
153
A
SER
154
n
154
SER
154
A
PRO
155
n
155
PRO
155
A
VAL
156
n
156
VAL
156
A
PHE
157
n
157
PHE
157
A
THR
158
n
158
THR
158
A
ALA
159
n
159
ALA
159
A
ASP
160
n
160
ASP
160
A
LEU
161
n
161
LEU
161
A
GLY
162
n
162
GLY
162
A
TYR
163
n
163
TYR
163
A
HIS
164
n
164
HIS
164
A
ALA
165
n
165
ALA
165
A
PRO
166
n
166
PRO
166
A
GLY
167
n
167
GLY
167
A
THR
168
n
168
THR
168
A
TYR
169
n
169
TYR
169
A
ASN
170
n
170
ASN
170
A
PHE
171
n
171
PHE
171
A
GLY
172
n
172
GLY
172
A
PHE
173
n
173
PHE
173
A
ILE
174
n
174
ILE
174
A
ASP
175
n
175
ASP
175
A
THR
176
n
176
THR
176
A
THR
177
n
177
THR
177
A
ALA
178
n
178
ALA
178
A
TYR
179
n
179
TYR
179
A
THR
180
n
180
THR
180
A
GLY
181
n
181
GLY
181
A
SER
182
n
182
SER
182
A
ILE
183
n
183
ILE
183
A
THR
184
n
184
THR
184
A
TYR
185
n
185
TYR
185
A
THR
186
n
186
THR
186
A
ALA
187
n
187
ALA
187
A
VAL
188
n
188
VAL
188
A
SER
189
n
189
SER
189
A
THR
190
n
190
THR
190
A
LYS
191
n
191
LYS
191
A
GLN
192
n
192
GLN
192
A
GLY
193
n
193
GLY
193
A
PHE
194
n
194
PHE
194
A
TRP
195
n
195
TRP
195
A
GLU
196
n
196
GLU
196
A
TRP
197
n
197
TRP
197
A
THR
198
n
198
THR
198
A
SER
199
n
199
SER
199
A
THR
200
n
200
THR
200
A
GLY
201
n
201
GLY
201
A
TYR
202
n
202
TYR
202
A
ALA
203
n
203
ALA
203
A
VAL
204
n
204
VAL
204
A
GLY
205
n
205
GLY
205
A
SER
206
n
206
SER
206
A
GLY
207
n
207
GLY
207
A
THR
208
n
208
THR
208
A
PHE
209
n
209
PHE
209
A
LYS
210
n
210
LYS
210
A
SER
211
n
211
SER
211
A
THR
212
n
212
THR
212
A
SER
213
n
213
SER
213
A
ILE
214
n
214
ILE
214
A
ASP
215
n
215
ASP
215
A
GLY
216
n
216
GLY
216
A
ILE
217
n
217
ILE
217
A
ALA
218
n
218
ALA
218
A
ASP
219
n
219
ASP
219
A
THR
220
n
220
THR
220
A
GLY
221
n
221
GLY
221
A
THR
222
n
222
THR
222
A
THR
223
n
223
THR
223
A
LEU
224
n
224
LEU
224
A
LEU
225
n
225
LEU
225
A
TYR
226
n
226
TYR
226
A
LEU
227
n
227
LEU
227
A
PRO
228
n
228
PRO
228
A
ALA
229
n
229
ALA
229
A
THR
230
n
230
THR
230
A
VAL
231
n
231
VAL
231
A
VAL
232
n
232
VAL
232
A
SER
233
n
233
SER
233
A
ALA
234
n
234
ALA
234
A
TYR
235
n
235
TYR
235
A
TRP
236
n
236
TRP
236
A
ALA
237
n
237
ALA
237
A
GLN
238
n
238
GLN
238
A
VAL
239
n
239
VAL
239
A
SER
240
n
240
SER
240
A
GLY
241
n
241
GLY
241
A
ALA
242
n
242
ALA
242
A
LYS
243
n
243
LYS
243
A
SER
244
n
244
SER
244
A
SER
245
n
245
SER
245
A
SER
246
n
246
SER
246
A
SER
247
n
247
SER
247
A
VAL
248
n
248
VAL
248
A
GLY
249
n
249
GLY
249
A
GLY
250
n
250
GLY
250
A
TYR
251
n
251
TYR
251
A
VAL
252
n
252
VAL
252
A
PHE
253
n
253
PHE
253
A
PRO
254
n
254
PRO
254
A
CYS
255
n
255
CYS
255
A
SER
256
n
256
SER
256
A
ALA
257
n
257
ALA
257
A
THR
258
n
258
THR
258
A
LEU
259
n
259
LEU
259
A
PRO
260
n
260
PRO
260
A
SER
261
n
261
SER
261
A
PHE
262
n
262
PHE
262
A
THR
263
n
263
THR
263
A
PHE
264
n
264
PHE
264
A
GLY
265
n
265
GLY
265
A
VAL
266
n
266
VAL
266
A
GLY
267
n
267
GLY
267
A
SER
268
n
268
SER
268
A
ALA
269
n
269
ALA
269
A
ARG
270
n
270
ARG
270
A
ILE
271
n
271
ILE
271
A
VAL
272
n
272
VAL
272
A
ILE
273
n
273
ILE
273
A
PRO
274
n
274
PRO
274
A
GLY
275
n
275
GLY
275
A
ASP
276
n
276
ASP
276
A
TYR
277
n
277
TYR
277
A
ILE
278
n
278
ILE
278
A
ASP
279
n
279
ASP
279
A
PHE
280
n
280
PHE
280
A
GLY
281
n
281
GLY
281
A
PRO
282
n
282
PRO
282
A
ILE
283
n
283
ILE
283
A
SER
284
n
284
SER
284
A
THR
285
n
285
THR
285
A
GLY
286
n
286
GLY
286
A
SER
287
n
287
SER
287
A
SER
288
n
288
SER
288
A
SER
289
n
289
SER
289
A
CYS
290
n
290
CYS
290
A
PHE
291
n
291
PHE
291
A
GLY
292
n
292
GLY
292
A
GLY
293
n
293
GLY
293
A
ILE
294
n
294
ILE
294
A
GLN
295
n
295
GLN
295
A
SER
296
n
296
SER
296
A
SER
297
n
297
SER
297
A
ALA
298
n
298
ALA
298
A
GLY
299
n
299
GLY
299
A
ILE
300
n
300
ILE
300
A
GLY
301
n
301
GLY
301
A
ILE
302
n
302
ILE
302
A
ASN
303
n
303
ASN
303
A
ILE
304
n
304
ILE
304
A
PHE
305
n
305
PHE
305
A
GLY
306
n
306
GLY
306
A
ASP
307
n
307
ASP
307
A
VAL
308
n
308
VAL
308
A
ALA
309
n
309
ALA
309
A
LEU
310
n
310
LEU
310
A
LYS
311
n
311
LYS
311
A
ALA
312
n
312
ALA
312
A
ALA
313
n
313
ALA
313
A
PHE
314
n
314
PHE
314
A
VAL
315
n
315
VAL
315
A
VAL
316
n
316
VAL
316
A
PHE
317
n
317
PHE
317
A
ASN
318
n
318
ASN
318
A
GLY
319
n
319
GLY
319
A
ALA
320
n
320
ALA
320
A
THR
321
n
321
THR
321
A
THR
322
n
322
THR
322
A
PRO
323
n
323
PRO
323
A
THR
324
n
324
THR
324
A
LEU
325
n
325
LEU
325
A
GLY
326
n
326
GLY
326
A
PHE
327
n
327
PHE
327
A
ALA
328
n
328
ALA
328
A
SER
329
n
329
SER
329
A
LYS
330
n
330
LYS
330
A
author_and_software_defined_assembly
PISA
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
A
N
LEU
70
A
N
LEU
70
A
O
VAL
89
A
O
VAL
89
A
O
SER
95
A
O
SER
95
A
N
GLN
22
A
N
GLN
22
A
O
ILE
18
A
O
ILE
18
A
N
THR
8
A
N
THR
8
A
N
THR
7
A
N
THR
7
A
O
GLY
167
A
O
GLY
167
A
O
ASN
170
A
O
ASN
170
A
N
THR
158
A
N
THR
158
A
N
PHE
157
A
N
PHE
157
A
O
PHE
317
A
O
PHE
317
A
N
PHE
314
A
N
PHE
314
A
O
ALA
328
A
O
ALA
328
A
O
LEU
325
A
O
LEU
325
A
N
THR
186
A
N
THR
186
A
N
LEU
70
A
N
LEU
70
A
O
VAL
89
A
O
VAL
89
A
N
TYR
90
A
N
TYR
90
A
O
VAL
106
A
O
VAL
106
A
O
GLU
107
A
O
GLU
107
A
N
LEU
41
A
N
LEU
41
A
N
TRP
42
A
N
TRP
42
A
O
LEU
125
A
O
LEU
125
A
O
LEU
126
A
O
LEU
126
A
N
ASP
35
A
N
ASP
35
A
O
GLN
28
A
O
GLN
28
A
N
ILE
23
A
N
ILE
23
A
O
ILE
18
A
O
ILE
18
A
N
THR
8
A
N
THR
8
A
N
THR
7
A
N
THR
7
A
O
GLY
167
A
O
GLY
167
A
O
ASN
170
A
O
ASN
170
A
N
THR
158
A
N
THR
158
A
N
PHE
157
A
N
PHE
157
A
O
PHE
317
A
O
PHE
317
A
N
PHE
314
A
N
PHE
314
A
O
ALA
328
A
O
ALA
328
A
O
LEU
325
A
O
LEU
325
A
N
THR
186
A
N
THR
186
A
O
ILE
273
A
O
ILE
273
A
N
PHE
262
A
N
PHE
262
A
O
THR
263
A
O
THR
263
A
N
ALA
203
A
N
ALA
203
A
N
TYR
202
A
N
TYR
202
A
O
LYS
210
A
O
LYS
210
A
N
ILE
217
A
N
ILE
217
A
O
PHE
305
A
O
PHE
305
A
O
ILE
304
A
O
ILE
304
A
N
TYR
226
A
N
TYR
226
A
N
LEU
225
A
N
LEU
225
A
O
GLN
295
A
O
GLN
295
A
N
SER
245
A
N
SER
245
A
O
GLY
250
A
O
GLY
250
A
N
PHE
253
A
N
PHE
253
A
O
CYS
290
A
O
CYS
290
A
O
PHE
291
A
O
PHE
291
A
N
GLY
281
A
N
GLY
281
1
A
CE
LYS
63
A
CE
LYS
63
1
Y
1
A
NZ
LYS
63
A
NZ
LYS
63
1
Y
1
A
CD
LYS
68
A
CD
LYS
68
1
Y
1
A
CE
LYS
68
A
CE
LYS
68
1
Y
1
A
NZ
LYS
68
A
NZ
LYS
68
1
Y
1
A
CE
LYS
110
A
CE
LYS
110
1
Y
1
A
NZ
LYS
110
A
NZ
LYS
110
1
Y
1
A
CD
LYS
111
A
CD
LYS
111
1
Y
1
A
CE
LYS
111
A
CE
LYS
111
1
Y
1
A
NZ
LYS
111
A
NZ
LYS
111
1
Y
1
A
CE
LYS
142
A
CE
LYS
142
1
Y
1
A
NZ
LYS
142
A
NZ
LYS
142
1
Y
1
A
CE
LYS
149
A
CE
LYS
149
1
Y
1
A
NZ
LYS
149
A
NZ
LYS
149
1
Y
1
A
CG
LYS
191
A
CG
LYS
191
1
Y
1
A
CD
LYS
191
A
CD
LYS
191
1
Y
1
A
CE
LYS
191
A
CE
LYS
191
1
Y
1
A
NZ
LYS
191
A
NZ
LYS
191
1
Y
1
A
CE
LYS
243
A
CE
LYS
243
1
Y
1
A
NZ
LYS
243
A
NZ
LYS
243
1
Y
44.810
15.1726
6.750
All 364 structures of this series were generated by an automated refinement pipeline and, thus, not refined to full convergence (e.g. since no manual (re-)building was performed, fragments are missing in the structural model even when present as indicated by the electron density)
0.1908
0.1544
0.1562
1.4400
28.1160
2848
54101
56949
5.0000
97.3500
0.1500
RANDOM
1
THROUGHOUT
1.370
MOLECULAR REPLACEMENT
19.9600
0.9000
1.1100
4Y5L
ML
FLAT BULK SOLVENT MODEL
1.4400
28.1160
165
2534
22.29
0
0
2369
330
0.008
2426
1.170
3329
0.070
399
0.006
424
10.513
783
0.2803
0.1972
1.4647
138
2617
2755
20
94.0000
0.2501
0.1783
1.4913
140
2651
2791
20
96.0000
0.2115
0.1601
1.5200
140
2665
2805
20
97.0000
0.2113
0.1554
1.5510
142
2705
2847
20
97.0000
0.2214
0.1547
1.5847
140
2662
2802
20
97.0000
0.2146
0.1510
1.6216
142
2692
2834
20
97.0000
0.2313
0.1459
1.6621
141
2677
2818
20
97.0000
0.1855
0.1449
1.7071
142
2688
2830
20
97.0000
0.2530
0.1464
1.7573
142
2708
2850
20
97.0000
0.1977
0.1463
1.8140
142
2696
2838
20
97.0000
0.1794
0.1465
1.8788
143
2711
2854
20
97.0000
0.2427
0.1508
1.9540
141
2684
2825
20
97.0000
0.1808
0.1456
2.0429
143
2714
2857
20
97.0000
0.1796
0.1410
2.1506
142
2703
2845
20
97.0000
0.1763
0.1416
2.2853
143
2714
2857
20
98.0000
0.1930
0.1528
2.4617
143
2718
2861
20
98.0000
0.1986
0.1574
2.7092
144
2744
2888
20
98.0000
0.1668
0.1605
3.1008
146
2767
2913
20
99.0000
0.1816
0.1574
3.9050
145
2764
2909
20
99.0000
0.1601
0.1613
28.1210
149
2821
2970
20
99.0000
11.240
1.440
42.702
5P69
56965
-3.000
0.999
0.061
0.070
0.976
1
15.140
238156
4.18
97.200
0.463
1.440
1.530
2.970
38328
9451
9032
0.864
0.529
1
0
95.600
0.315
1.530
1.630
4.370
36492
8867
8588
0.929
0.360
1
0
96.900
0.219
1.630
1.760
6.320
33947
8239
7991
0.963
0.250
1
0
97.000
0.131
1.760
1.930
10.590
31018
7585
7380
0.985
0.150
1
0
97.300
0.077
1.930
2.160
17.690
27718
6928
6736
0.994
0.089
1
0
97.200
0.059
2.160
2.490
22.520
24357
6085
5964
0.996
0.068
1
0
98.000
0.040
2.490
3.050
29.490
20841
5158
5069
0.998
0.046
1
0
98.300
0.027
3.050
4.300
41.100
16308
4017
3969
0.999
0.031
1
0
98.800
0.022
4.300
46.180
9147
2278
2236
0.999
0.025
1
0
98.200
data scaling
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/XDS.html
XDS
package
refinement
Paul D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
phasing
Randy J. Read
cimr-phaser@lists.cam.ac.uk
Tue Apr 7 01:51:31 2015 (svn revision: 6786)
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
2.5.7
data extraction
PDB
deposit@deposit.rcsb.org
June. 20, 2015
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.20
data reduction
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/XDS.html
XDS
package
All 364 structures of this series were generated by an automated refinement pipeline and, thus, not refined to full convergence (e.g. since no manual (re-)building was performed, fragments are missing in the structural model even when present as indicated by the electron density)
Automated refinement of diffraction data obtained from an endothiapepsin crystal treated with fragment 270
1
N
N
2
N
N
A
THR
49
A
THR
49
HELX_P
A
VAL
53
A
VAL
53
5
AA1
5
A
THR
60
A
THR
60
HELX_P
A
SER
64
A
SER
64
5
AA2
5
A
SER
113
A
SER
113
HELX_P
A
ASP
119
A
ASP
119
1
AA3
7
A
PHE
130
A
PHE
130
HELX_P
A
ASN
134
A
ASN
134
5
AA4
5
A
THR
143
A
THR
143
HELX_P
A
LYS
149
A
LYS
149
1
AA5
7
A
ALA
150
A
ALA
150
HELX_P
A
LEU
152
A
LEU
152
5
AA6
3
A
PRO
228
A
PRO
228
HELX_P
A
ALA
237
A
ALA
237
1
AA7
10
A
PRO
274
A
PRO
274
HELX_P
A
TYR
277
A
TYR
277
5
AA8
4
A
GLY
306
A
GLY
306
HELX_P
A
LYS
311
A
LYS
311
1
AA9
6
disulf
2.064
A
CYS
255
A
SG
CYS
255
1_555
A
CYS
290
A
SG
CYS
290
1_555
HYDROLASE
fragment screening, method development, aspartic protease, HYDROLASE
A
THR
25
A
THR
25
1
A
PRO
26
A
PRO
26
-5.80
A
SER
137
A
SER
137
1
A
PRO
138
A
PRO
138
5.33
CARP_CRYPA
UNP
1
90
P11838
STGSATTTPIDSLDDAYITPVQIGTPAQTLNLDFDTGSSDLWVFSSETTASEVDGQTIYTPSKSTTAKLLSGATWSISYG
DGSSSSGDVYTDTVSVGGLTVTGQAVESAKKVSSSFTEDSTIDGLLGLAFSTLNTVSPTQQKTFFDNAKASLDSPVFTAD
LGYHAPGTYNFGFIDTTAYTGSITYTAVSTKQGFWEWTSTGYAVGSGTFKSTSIDGIADTGTTLLYLPATVVSAYWAQVS
GAKSSSSVGGYVFPCSATLPSFTFGVGSARIVIPGDYIDFGPISTGSSSCFGGIQSSAGIGINIFGDVALKAAFVVFNGA
TTPTLGFASK
90
419
5OYQ
1
330
P11838
A
1
1
330
9
13
7
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
A
LYS
68
A
LYS
68
A
SER
78
A
SER
78
A
SER
84
A
SER
84
A
VAL
96
A
VAL
96
A
TYR
17
A
TYR
17
A
ILE
23
A
ILE
23
A
GLY
3
A
GLY
3
A
PRO
9
A
PRO
9
A
GLY
167
A
GLY
167
A
PHE
171
A
PHE
171
A
VAL
156
A
VAL
156
A
ASP
160
A
ASP
160
A
PHE
314
A
PHE
314
A
ASN
318
A
ASN
318
A
THR
324
A
THR
324
A
ALA
328
A
ALA
328
A
THR
184
A
THR
184
A
ALA
187
A
ALA
187
A
LYS
68
A
LYS
68
A
SER
78
A
SER
78
A
SER
84
A
SER
84
A
VAL
96
A
VAL
96
A
LEU
99
A
LEU
99
A
VAL
112
A
VAL
112
A
LEU
41
A
LEU
41
A
VAL
43
A
VAL
43
A
GLY
124
A
GLY
124
A
GLY
127
A
GLY
127
A
GLN
28
A
GLN
28
A
ASP
35
A
ASP
35
A
TYR
17
A
TYR
17
A
ILE
23
A
ILE
23
A
GLY
3
A
GLY
3
A
PRO
9
A
PRO
9
A
GLY
167
A
GLY
167
A
PHE
171
A
PHE
171
A
VAL
156
A
VAL
156
A
ASP
160
A
ASP
160
A
PHE
314
A
PHE
314
A
ASN
318
A
ASN
318
A
THR
324
A
THR
324
A
ALA
328
A
ALA
328
A
THR
184
A
THR
184
A
ALA
187
A
ALA
187
A
ALA
269
A
ALA
269
A
ILE
273
A
ILE
273
A
PHE
262
A
PHE
262
A
VAL
266
A
VAL
266
A
GLU
196
A
GLU
196
A
VAL
204
A
VAL
204
A
LYS
210
A
LYS
210
A
ALA
218
A
ALA
218
A
ASN
303
A
ASN
303
A
PHE
305
A
PHE
305
A
LEU
225
A
LEU
225
A
LEU
227
A
LEU
227
A
ILE
294
A
ILE
294
A
SER
296
A
SER
296
A
LYS
243
A
LYS
243
A
SER
245
A
SER
245
A
GLY
250
A
GLY
250
A
PRO
254
A
PRO
254
A
SER
289
A
SER
289
A
GLY
292
A
GLY
292
A
ASP
279
A
ASP
279
A
PRO
282
A
PRO
282
4
P 1 21 1