0.011688
0.006748
0.000000
0.000000
0.013496
0.000000
0.000000
0.000000
0.019920
0.00000
0.00000
0.00000
Shenoy, R.T.
Sivaraman, J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
85.557
85.557
50.201
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
C31 H34 N4 O5
542.625
Nalpha-[(benzyloxy)carbonyl]-N-[(1S)-1-(4-tert-butoxybenzyl)-3-diazo-2-oxopropyl]-L-phenylalaninamide
Z-Phe-Tyr(t-Bu)-diazomethylketone
peptide-like
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
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
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
N
118
N
H
N
119
N
H
N
120
N
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
N
N
128
N
C
N
129
N
C
N
130
N
O
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
Y
142
N
C
Y
143
N
N
Y
144
N
C
Y
145
N
C
Y
146
N
N
N
147
N
O
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
C
N
159
N
O
N
160
N
O
N
161
N
C
Y
162
N
C
Y
163
N
C
Y
164
N
C
Y
165
N
C
Y
166
N
C
Y
167
N
C
N
168
N
N
N
169
S
C
N
170
N
C
N
171
N
O
N
172
N
C
Y
173
N
C
Y
174
N
C
Y
175
N
C
Y
176
N
C
Y
177
N
C
Y
178
N
C
N
179
N
N
Y
180
N
C
N
181
N
O
Y
182
N
C
N
183
N
C
N
184
N
C
N
185
N
C
N
186
N
C
N
187
N
C
N
188
N
C
N
189
S
C
Y
190
N
C
Y
191
N
C
Y
192
N
C
Y
193
N
C
N
194
N
O
N
195
N
C
N
196
N
N
N
197
N
N
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
H
N
232
N
N
N
233
S
C
N
234
N
C
N
235
N
O
N
236
S
C
N
237
N
C
N
238
N
C
N
239
N
C
N
240
N
O
N
241
N
H
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
N
N
255
S
C
N
256
N
C
N
257
N
O
N
258
N
C
N
259
N
C
N
260
N
C
N
261
N
C
N
262
N
O
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
N
N
277
S
C
N
278
N
C
N
279
N
O
N
280
N
C
N
281
N
C
N
282
N
C
N
283
N
C
N
284
N
N
N
285
N
O
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
N
N
302
S
C
N
303
N
C
N
304
N
O
N
305
N
C
N
306
N
C
N
307
N
S
N
308
N
C
N
309
N
O
N
310
N
H
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
H
N
319
N
H
N
320
N
H
N
321
N
N
N
322
S
C
N
323
N
C
N
324
N
O
N
325
N
C
Y
326
N
C
Y
327
N
C
Y
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
C
N
332
N
O
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
N
N
345
S
C
N
346
N
C
N
347
N
O
N
348
N
C
N
349
N
C
N
350
N
C
N
351
N
O
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
N
N
362
S
C
N
363
N
C
N
364
N
O
N
365
N
C
N
366
N
O
N
367
N
O
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
N
N
376
S
C
N
377
N
C
N
378
N
O
N
379
R
C
N
380
N
O
N
381
N
C
N
382
N
O
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
N
N
393
S
C
N
394
N
C
N
395
N
O
N
396
N
C
Y
397
N
C
Y
398
N
C
Y
399
N
C
Y
400
N
N
Y
401
N
C
Y
402
N
C
Y
403
N
C
Y
404
N
C
Y
405
N
C
N
406
N
O
N
407
N
H
N
408
N
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
N
N
420
S
C
N
421
N
C
N
422
N
O
N
423
N
C
Y
424
N
C
Y
425
N
C
Y
426
N
C
Y
427
N
C
Y
428
N
C
Y
429
N
C
N
430
N
O
N
431
N
O
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
N
N
444
S
C
N
445
N
C
N
446
N
O
N
447
N
C
N
448
N
C
N
449
N
C
N
450
N
O
N
451
N
H
N
452
N
H
N
453
N
H
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
doub
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
Y
140
N
sing
Y
141
N
doub
Y
142
N
doub
N
143
N
sing
Y
144
N
sing
N
145
N
sing
Y
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
doub
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
Y
161
N
doub
Y
162
N
sing
Y
163
N
doub
N
164
N
sing
N
165
N
sing
Y
166
N
sing
N
167
N
sing
Y
168
N
doub
N
169
N
sing
Y
170
N
sing
N
171
N
sing
N
172
N
doub
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
Y
179
N
doub
N
180
N
sing
N
181
N
sing
Y
182
N
sing
N
183
N
sing
N
184
N
doub
Y
185
N
doub
N
186
N
sing
Y
187
N
sing
Y
188
N
doub
N
189
N
sing
Y
190
N
sing
N
191
N
sing
Y
192
N
doub
N
193
N
sing
Y
194
N
doub
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
Y
215
N
sing
Y
216
N
doub
N
217
N
sing
Y
218
N
sing
N
219
N
sing
Y
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
doub
N
224
N
sing
N
225
N
doub
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
doub
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
doub
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
doub
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
doub
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
doub
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
Y
322
N
doub
Y
323
N
sing
Y
324
N
sing
N
325
N
sing
Y
326
N
doub
N
327
N
sing
Y
328
N
doub
N
329
N
sing
Y
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
doub
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
doub
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
doub
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
Y
391
N
doub
Y
392
N
sing
Y
393
N
sing
N
394
N
sing
Y
395
N
doub
Y
396
N
sing
Y
397
N
sing
N
398
N
sing
Y
399
N
sing
Y
400
N
doub
N
401
N
sing
Y
402
N
doub
N
403
N
sing
Y
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
doub
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
Y
419
N
doub
Y
420
N
sing
Y
421
N
sing
N
422
N
sing
Y
423
N
doub
N
424
N
sing
Y
425
N
doub
N
426
N
sing
Y
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
doub
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
US
J.Struct.Biol.
JSBIEM
0803
1047-8477
173
14
19
10.1016/j.jsb.2010.09.007
20850545
Structural basis for reversible and irreversible inhibition of human cathepsin L by their respective dipeptidyl glyoxal and diazomethylketone inhibitors.
2011
10.2210/pdb3of9/pdb
pdb_00003of9
100
1
CCD
2008-03-28
ADSC QUANTUM 315
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
X29A
NSLS
1.5418
SYNCHROTRON
NSLS BEAMLINE X29A
24320.814
Cathepsin L1
3.4.22.15
Cathepsin L
1
man
polymer
542.625
Nalpha-[(benzyloxy)carbonyl]-N-[(1S)-1-(4-tert-butoxybenzyl)-3-diazo-2-oxopropyl]-L-phenylalaninamide
1
syn
non-polymer
Major excreted protein, MEP, Cathepsin L1 heavy chain, Cathepsin L1 light chain
no
no
EAPRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQD
NGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSE
DMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV
EAPRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQD
NGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSE
DMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV
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
human
sample
CTSL1, CTSL
9606
Homo sapiens
4922
Pichia pastoris
Plasmid
pPIC9
1
2.15
42.85
VAPOR DIFFUSION, HANGING DROP
5.2
30%( w/v) PEG 8K and 200mM Ammonium sulfate, pH 5.2, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K
298.0
pdbx_unobs_or_zero_occ_atoms
software
software
struct_conn
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_unobs_or_zero_occ_atoms
struct_site
repository
Initial release
Version format compliance
Other
Advisory
Refinement description
Data collection
Derived calculations
Refinement description
Advisory
Data collection
Database references
Derived calculations
Refinement description
1
0
2010-12-08
1
1
2011-07-13
1
2
2012-12-12
1
3
2017-11-08
1
4
2019-07-17
1
5
2023-09-06
_software.classification
_software.contact_author
_software.contact_author_email
_software.location
_software.name
_software.type
_software.version
_struct_conn.pdbx_leaving_atom_flag
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2010-08-14
REL
REL
I0X
Nalpha-[(benzyloxy)carbonyl]-N-[(1S)-1-(4-tert-butoxybenzyl)-3-diazo-2-oxopropyl]-L-phenylalaninamide
1CS8
PDB
experimental model
Enzyme inhibitor
NALPHA-[(BENZYLOXY)CARBONYL]-N-[(1S)-1-(4-TERT-BUTOXYBENZYL)-3-DIAZO-2-OXOPROPYL]-L-PHENYLALANINAMIDE
Peptide-like
I0X
501
2
I0X
I0X
501
A
GLU
1
n
1
GLU
1
A
ALA
2
n
2
ALA
2
A
PRO
3
n
3
PRO
3
A
ARG
4
n
4
ARG
4
A
SER
5
n
5
SER
5
A
VAL
6
n
6
VAL
6
A
ASP
7
n
7
ASP
7
A
TRP
8
n
8
TRP
8
A
ARG
9
n
9
ARG
9
A
GLU
10
n
10
GLU
10
A
LYS
11
n
11
LYS
11
A
GLY
12
n
12
GLY
12
A
TYR
13
n
13
TYR
13
A
VAL
14
n
14
VAL
14
A
THR
15
n
15
THR
15
A
PRO
16
n
16
PRO
16
A
VAL
17
n
17
VAL
17
A
LYS
18
n
18
LYS
18
A
ASN
19
n
19
ASN
19
A
GLN
20
n
20
GLN
20
A
GLY
21
n
21
GLY
21
A
GLN
22
n
22
GLN
22
A
CYS
23
n
23
CYS
23
A
GLY
24
n
24
GLY
24
A
SER
25
n
25
SER
25
A
CYS
26
n
26
CYS
26
A
TRP
27
n
27
TRP
27
A
ALA
28
n
28
ALA
28
A
PHE
29
n
29
PHE
29
A
SER
30
n
30
SER
30
A
ALA
31
n
31
ALA
31
A
THR
32
n
32
THR
32
A
GLY
33
n
33
GLY
33
A
ALA
34
n
34
ALA
34
A
LEU
35
n
35
LEU
35
A
GLU
36
n
36
GLU
36
A
GLY
37
n
37
GLY
37
A
GLN
38
n
38
GLN
38
A
MET
39
n
39
MET
39
A
PHE
40
n
40
PHE
40
A
ARG
41
n
41
ARG
41
A
LYS
42
n
42
LYS
42
A
THR
43
n
43
THR
43
A
GLY
44
n
44
GLY
44
A
ARG
45
n
45
ARG
45
A
LEU
46
n
46
LEU
46
A
ILE
47
n
47
ILE
47
A
SER
48
n
48
SER
48
A
LEU
49
n
49
LEU
49
A
SER
50
n
50
SER
50
A
GLU
51
n
51
GLU
51
A
GLN
52
n
52
GLN
52
A
ASN
53
n
53
ASN
53
A
LEU
54
n
54
LEU
54
A
VAL
55
n
55
VAL
55
A
ASP
56
n
56
ASP
56
A
CYS
57
n
57
CYS
57
A
SER
58
n
58
SER
58
A
GLY
59
n
59
GLY
59
A
PRO
60
n
60
PRO
60
A
GLN
61
n
61
GLN
61
A
GLY
62
n
62
GLY
62
A
ASN
63
n
63
ASN
63
A
GLU
64
n
64
GLU
64
A
GLY
65
n
65
GLY
65
A
CYS
66
n
66
CYS
66
A
ASN
67
n
67
ASN
67
A
GLY
68
n
68
GLY
68
A
GLY
69
n
69
GLY
69
A
LEU
70
n
70
LEU
70
A
MET
71
n
71
MET
71
A
ASP
72
n
72
ASP
72
A
TYR
73
n
73
TYR
73
A
ALA
74
n
74
ALA
74
A
PHE
75
n
75
PHE
75
A
GLN
76
n
76
GLN
76
A
TYR
77
n
77
TYR
77
A
VAL
78
n
78
VAL
78
A
GLN
79
n
79
GLN
79
A
ASP
80
n
80
ASP
80
A
ASN
81
n
81
ASN
81
A
GLY
82
n
82
GLY
82
A
GLY
83
n
83
GLY
83
A
LEU
84
n
84
LEU
84
A
ASP
85
n
85
ASP
85
A
SER
86
n
86
SER
86
A
GLU
87
n
87
GLU
87
A
GLU
88
n
88
GLU
88
A
SER
89
n
89
SER
89
A
TYR
90
n
90
TYR
90
A
PRO
91
n
91
PRO
91
A
TYR
92
n
92
TYR
92
A
GLU
93
n
93
GLU
93
A
ALA
94
n
94
ALA
94
A
THR
95
n
95
THR
95
A
GLU
96
n
96
GLU
96
A
GLU
97
n
97
GLU
97
A
SER
98
n
98
SER
98
A
CYS
99
n
99
CYS
99
A
LYS
100
n
100
LYS
100
A
TYR
101
n
101
TYR
101
A
ASN
102
n
102
ASN
102
A
PRO
103
n
103
PRO
103
A
LYS
104
n
104
LYS
104
A
TYR
105
n
105
TYR
105
A
SER
106
n
106
SER
106
A
VAL
107
n
107
VAL
107
A
ALA
108
n
108
ALA
108
A
ASN
109
n
109
ASN
109
A
ASP
110
n
110
ASP
110
A
THR
111
n
111
THR
111
A
GLY
112
n
112
GLY
112
A
PHE
113
n
113
PHE
113
A
VAL
114
n
114
VAL
114
A
ASP
115
n
115
ASP
115
A
ILE
116
n
116
ILE
116
A
PRO
117
n
117
PRO
117
A
LYS
118
n
118
LYS
118
A
GLN
119
n
119
GLN
119
A
GLU
120
n
120
GLU
120
A
LYS
121
n
121
LYS
121
A
ALA
122
n
122
ALA
122
A
LEU
123
n
123
LEU
123
A
MET
124
n
124
MET
124
A
LYS
125
n
125
LYS
125
A
ALA
126
n
126
ALA
126
A
VAL
127
n
127
VAL
127
A
ALA
128
n
128
ALA
128
A
THR
129
n
129
THR
129
A
VAL
130
n
130
VAL
130
A
GLY
131
n
131
GLY
131
A
PRO
132
n
132
PRO
132
A
ILE
133
n
133
ILE
133
A
SER
134
n
134
SER
134
A
VAL
135
n
135
VAL
135
A
ALA
136
n
136
ALA
136
A
ILE
137
n
137
ILE
137
A
ASP
138
n
138
ASP
138
A
ALA
139
n
139
ALA
139
A
GLY
140
n
140
GLY
140
A
HIS
141
n
141
HIS
141
A
GLU
142
n
142
GLU
142
A
SER
143
n
143
SER
143
A
PHE
144
n
144
PHE
144
A
LEU
145
n
145
LEU
145
A
PHE
146
n
146
PHE
146
A
TYR
147
n
147
TYR
147
A
LYS
148
n
148
LYS
148
A
GLU
149
n
149
GLU
149
A
GLY
150
n
150
GLY
150
A
ILE
151
n
151
ILE
151
A
TYR
152
n
152
TYR
152
A
PHE
153
n
153
PHE
153
A
GLU
154
n
154
GLU
154
A
PRO
155
n
155
PRO
155
A
ASP
156
n
156
ASP
156
A
CYS
157
n
157
CYS
157
A
SER
158
n
158
SER
158
A
SER
159
n
159
SER
159
A
GLU
160
n
160
GLU
160
A
ASP
161
n
161
ASP
161
A
MET
162
n
162
MET
162
A
ASP
163
n
163
ASP
163
A
HIS
164
n
164
HIS
164
A
GLY
165
n
165
GLY
165
A
VAL
166
n
166
VAL
166
A
LEU
167
n
167
LEU
167
A
VAL
168
n
168
VAL
168
A
VAL
169
n
169
VAL
169
A
GLY
170
n
170
GLY
170
A
TYR
171
n
171
TYR
171
A
GLY
172
n
172
GLY
172
A
PHE
173
n
173
PHE
173
A
GLU
174
n
174
GLU
174
A
SER
175
n
175
SER
175
A
THR
176
n
176
THR
176
A
GLU
177
n
177
GLU
177
A
SER
178
n
178
SER
178
A
ASP
179
n
179
ASP
179
A
ASN
180
n
180
ASN
180
A
ASN
181
n
181
ASN
181
A
LYS
182
n
182
LYS
182
A
TYR
183
n
183
TYR
183
A
TRP
184
n
184
TRP
184
A
LEU
185
n
185
LEU
185
A
VAL
186
n
186
VAL
186
A
LYS
187
n
187
LYS
187
A
ASN
188
n
188
ASN
188
A
SER
189
n
189
SER
189
A
TRP
190
n
190
TRP
190
A
GLY
191
n
191
GLY
191
A
GLU
192
n
192
GLU
192
A
GLU
193
n
193
GLU
193
A
TRP
194
n
194
TRP
194
A
GLY
195
n
195
GLY
195
A
MET
196
n
196
MET
196
A
GLY
197
n
197
GLY
197
A
GLY
198
n
198
GLY
198
A
TYR
199
n
199
TYR
199
A
VAL
200
n
200
VAL
200
A
LYS
201
n
201
LYS
201
A
MET
202
n
202
MET
202
A
ALA
203
n
203
ALA
203
A
LYS
204
n
204
LYS
204
A
ASP
205
n
205
ASP
205
A
ARG
206
n
206
ARG
206
A
ARG
207
n
207
ARG
207
A
ASN
208
n
208
ASN
208
A
HIS
209
n
209
HIS
209
A
CYS
210
n
210
CYS
210
A
GLY
211
n
211
GLY
211
A
ILE
212
n
212
ILE
212
A
ALA
213
n
213
ALA
213
A
SER
214
n
214
SER
214
A
ALA
215
n
215
ALA
215
A
ALA
216
n
216
ALA
216
A
SER
217
n
217
SER
217
A
TYR
218
n
218
TYR
218
A
PRO
219
n
219
PRO
219
A
THR
220
n
220
THR
220
A
VAL
221
n
221
VAL
221
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
VAL
6
A
N
VAL
6
A
O
TYR
171
A
O
TYR
171
A
O
VAL
168
A
O
VAL
168
A
N
ILE
133
A
N
ILE
133
A
N
VAL
6
A
N
VAL
6
A
O
TYR
171
A
O
TYR
171
A
N
LEU
167
A
N
LEU
167
A
O
LYS
187
A
O
LYS
187
A
N
TRP
184
A
N
TRP
184
A
O
MET
202
A
O
MET
202
A
O
LYS
201
A
O
LYS
201
A
N
TYR
152
A
N
TYR
152
A
N
LEU
84
A
N
LEU
84
A
O
VAL
107
A
O
VAL
107
A
N
VAL
114
A
N
VAL
114
A
O
TYR
218
A
O
TYR
218
1
A
O
GLU
1
A
O
GLU
1
0
Y
1
A
OD1
ASN
109
A
OD1
ASN
109
0
Y
1
A
CD
GLN
119
A
CD
GLN
119
0
Y
1
A
CA
GLU
177
A
CA
GLU
177
0
Y
1
A
CG
GLU
177
A
CG
GLU
177
0
Y
1
A
ALA
2
68.00
162.27
1
A
LYS
148
-131.51
-49.41
1
A
THR
176
-54.15
-93.11
1
A
SER
178
-169.47
102.90
1
A
ASP
179
160.80
-48.20
1
A
ARG
206
-119.97
57.11
1
A
ALA
215
-140.84
55.02
CNS_TOPPAR:protein_rep.param
CNS_TOPPAR:water_rep.param
inh3.par
0.0211
-0.0000
0.0000
0.0211
-0.0000
-0.0422
0.2494
0.2244
0.2268
1.761
29.809
1930
20017
9.64
95.83
1.000
0.500
0.23
1
0.12
MOLECULAR REPLACEMENT
23.43
0.90
1.11
1CS8
ML
FLAT BULK SOLVENT MODEL
34.709
0.434
1.761
29.809
0
1744
38
0
1706
0.007
1792
1.118
2419
18.154
647
0.074
238
0.005
322
0.2937
0.2374
1.8048
122
1056
78.00
0.2587
0.1991
1.8536
129
1190
91.00
0.2172
0.1953
1.9081
132
1275
93.00
0.2305
0.1925
1.9697
134
1258
95.00
0.2524
0.1992
2.0401
141
1301
97.00
0.2714
0.2154
2.1217
136
1286
96.00
0.2391
0.2136
2.2183
143
1309
98.00
0.2408
0.2187
2.3352
137
1319
98.00
0.2584
0.2283
2.4814
143
1335
99.00
0.2487
0.2448
2.6729
140
1331
98.00
0.2601
0.2305
2.9417
145
1336
99.00
0.2844
0.2368
3.3668
141
1338
100.00
0.2195
0.2096
4.2399
145
1366
100.00
0.2402
0.2360
29.8132
142
1387
99.00
1.7
50
3OF9
22014
1.0
1.0
1
95
refinement
PHENIX
1.6_289
data scaling
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
SCALEPACK
package
phasing
Alexei Vaguine
alexei@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/molrep.html
MOLREP
program
refinement
Axel T. Brunger
axel.brunger@yale.edu
Fortran_77
http://cns-online.org/
CNS
package
data extraction
PDB
deposit@deposit.rcsb.org
June 10, 2010
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.10
data collection
CBASS
data reduction
HKL-2000
data scaling
HKL-2000
data reduction
Zbyszek Otwinowski
hkl@hkl-xray.com
http://www.hkl-xray.com/
DENZO
package
Structural Basis for Irreversible Inhibition of Human Cathepsin L by a Diazomethylketone Inhibitor
1
N
N
2
N
N
A
ARG
9
A
ARG
9
HELX_P
A
GLY
12
A
GLY
12
5
1
4
A
SER
25
A
SER
25
HELX_P
A
GLY
44
A
GLY
44
1
2
20
A
SER
50
A
SER
50
HELX_P
A
SER
58
A
SER
58
1
3
9
A
GLY
59
A
GLY
59
HELX_P
A
GLY
62
A
GLY
62
5
4
4
A
GLU
64
A
GLU
64
HELX_P
A
GLY
68
A
GLY
68
5
5
5
A
LEU
70
A
LEU
70
HELX_P
A
GLY
82
A
GLY
82
1
6
13
A
ASN
102
A
ASN
102
HELX_P
A
LYS
104
A
LYS
104
5
7
3
A
GLN
119
A
GLN
119
HELX_P
A
VAL
130
A
VAL
130
1
8
12
A
HIS
141
A
HIS
141
HELX_P
A
PHE
146
A
PHE
146
1
9
6
A
ASN
208
A
ASN
208
HELX_P
A
ILE
212
A
ILE
212
5
10
5
disulf
2.046
A
CYS
23
A
SG
CYS
23
1_555
A
CYS
66
A
SG
CYS
66
1_555
disulf
2.039
A
CYS
57
A
SG
CYS
57
1_555
A
CYS
99
A
SG
CYS
99
1_555
disulf
2.041
A
CYS
157
A
SG
CYS
157
1_555
A
CYS
210
A
SG
CYS
210
1_555
covale
1.794
one
A
CYS
26
A
SG
CYS
26
1_555
A
I0X
501
B
C31
I0X
1_555
HYDROLASE/HYDROLASE INHIBITOR
HYDROLASE-HYDROLASE INHIBITOR complex
CATL1_HUMAN
UNP
1
113
P07711
EAPRSVDWREKGYVTPVKNQGQCGSCWAFSATGALEGQMFRKTGRLISLSEQNLVDCSGPQGNEGCNGGLMDYAFQYVQD
NGGLDSEESYPYEATEESCKYNPKYSVANDTGFVDIPKQEKALMKAVATVGPISVAIDAGHESFLFYKEGIYFEPDCSSE
DMDHGVLVVGYGFESTESDNNKYWLVKNSWGEEWGMGGYVKMAKDRRNHCGIASAASYPTV
113
333
3OF9
1
221
P07711
A
1
1
221
3
5
2
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
VAL
6
A
VAL
6
A
ASP
7
A
ASP
7
A
HIS
164
A
HIS
164
A
PHE
173
A
PHE
173
A
ILE
133
A
ILE
133
A
ILE
137
A
ILE
137
A
VAL
6
A
VAL
6
A
ASP
7
A
ASP
7
A
HIS
164
A
HIS
164
A
PHE
173
A
PHE
173
A
LYS
182
A
LYS
182
A
LYS
187
A
LYS
187
A
TYR
199
A
TYR
199
A
ALA
203
A
ALA
203
A
ILE
151
A
ILE
151
A
TYR
152
A
TYR
152
A
LEU
84
A
LEU
84
A
ASP
85
A
ASP
85
A
SER
106
A
SER
106
A
ALA
108
A
ALA
108
A
PHE
113
A
PHE
113
A
ASP
115
A
ASP
115
A
SER
217
A
SER
217
A
PRO
219
A
PRO
219
BINDING SITE FOR RESIDUE I0X A 501
A
I0X
501
Software
21
A
ARG
9
A
ARG
9
21
5_555
A
GLU
10
A
GLU
10
21
5_555
A
GLY
12
A
GLY
12
21
5_555
A
GLN
20
A
GLN
20
21
1_555
A
GLY
24
A
GLY
24
21
1_555
A
SER
25
A
SER
25
21
1_555
A
CYS
26
A
CYS
26
21
1_555
A
TRP
27
A
TRP
27
21
1_555
A
GLY
62
A
GLY
62
21
1_555
A
GLU
64
A
GLU
64
21
1_555
A
GLY
68
A
GLY
68
21
1_555
A
GLY
69
A
GLY
69
21
1_555
A
LEU
70
A
LEU
70
21
1_555
A
MET
71
A
MET
71
21
1_555
A
ALA
136
A
ALA
136
21
1_555
A
ALA
139
A
ALA
139
21
1_555
A
MET
162
A
MET
162
21
1_555
A
ASP
163
A
ASP
163
21
1_555
A
HIS
164
A
HIS
164
21
1_555
A
TRP
190
A
TRP
190
21
1_555
A
GLU
192
A
GLU
192
21
5_555
170
P 65