0.023317
0.000000
0.000000
0.000000
0.010337
0.000000
0.000000
0.000000
0.020047
0.00000
0.00000
0.00000
Janowski, R.
Kozak, M.
Jankowska, E.
Grzonka, Z.
Jaskolski, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
42.89
96.74
49.88
C H2 N2
42.040
diazomethane
DIAZOMETHYL 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
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
C8 H7 Cl O2
170.593
benzyl chlorocarbonate
non-polymer
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
C
N
2
N
N
N
3
N
N
N
4
N
H
N
5
N
H
N
6
N
N
N
7
S
C
N
8
N
C
N
9
N
O
N
10
N
C
N
11
N
O
N
12
N
H
N
13
N
H
N
14
N
H
N
15
N
H
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
N
N
20
S
C
N
21
N
C
N
22
N
O
N
23
N
C
N
24
N
C
N
25
N
C
N
26
N
N
N
27
N
C
N
28
N
N
N
29
N
N
N
30
N
O
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
H
N
42
N
H
N
43
N
H
N
44
N
H
N
45
N
H
N
46
N
N
N
47
S
C
N
48
N
C
N
49
N
O
N
50
N
C
N
51
N
C
N
52
N
O
N
53
N
N
N
54
N
O
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
N
N
64
S
C
N
65
N
C
N
66
N
O
N
67
N
C
N
68
N
C
N
69
N
O
N
70
N
O
N
71
N
O
N
72
N
H
N
73
N
H
N
74
N
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
N
N
80
R
C
N
81
N
C
N
82
N
O
N
83
N
C
N
84
N
S
N
85
N
O
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
N
N
94
S
C
N
95
N
C
N
96
N
O
N
97
N
C
N
98
N
C
N
99
N
C
N
100
N
O
N
101
N
N
N
102
N
O
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
H
N
109
N
H
N
110
N
H
N
111
N
H
N
112
N
H
N
113
N
N
N
114
S
C
N
115
N
C
N
116
N
O
N
117
N
C
N
118
N
C
N
119
N
C
N
120
N
O
N
121
N
O
N
122
N
O
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
N
N
133
N
C
N
134
N
C
N
135
N
O
N
136
N
O
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
N
N
143
S
C
N
144
N
C
N
145
N
O
N
146
N
C
Y
147
N
C
Y
148
N
N
Y
149
N
C
Y
150
N
C
Y
151
N
N
N
152
N
O
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
O
N
164
N
H
N
165
N
H
N
166
N
N
N
167
S
C
N
168
N
C
N
169
N
O
N
170
S
C
N
171
N
C
N
172
N
C
N
173
N
C
N
174
N
O
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
N
N
189
S
C
N
190
N
C
N
191
N
O
N
192
N
C
N
193
N
C
N
194
N
C
N
195
N
C
N
196
N
O
N
197
N
H
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
N
N
211
S
C
N
212
N
C
N
213
N
O
N
214
N
C
N
215
N
C
N
216
N
C
N
217
N
C
N
218
N
N
N
219
N
O
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
H
N
233
N
H
N
234
N
H
N
235
N
N
N
236
S
C
N
237
N
C
N
238
N
O
N
239
N
C
Y
240
N
C
Y
241
N
C
Y
242
N
C
Y
243
N
C
Y
244
N
C
Y
245
N
C
N
246
N
O
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
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
C
N
259
N
O
N
260
N
O
N
261
N
C
Y
262
N
C
Y
263
N
C
Y
264
N
C
Y
265
N
C
Y
266
N
C
Y
267
N
C
N
268
N
CL
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
O
N
284
N
H
N
285
N
H
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
N
N
294
S
C
N
295
N
C
N
296
N
O
N
297
N
C
N
298
N
O
N
299
N
O
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
H
N
305
N
H
N
306
N
H
N
307
N
N
N
308
S
C
N
309
N
C
N
310
N
O
N
311
R
C
N
312
N
O
N
313
N
C
N
314
N
O
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
H
N
322
N
H
N
323
N
H
N
324
N
N
N
325
S
C
N
326
N
C
N
327
N
O
N
328
N
C
Y
329
N
C
Y
330
N
C
Y
331
N
C
Y
332
N
N
Y
333
N
C
Y
334
N
C
Y
335
N
C
Y
336
N
C
Y
337
N
C
N
338
N
O
N
339
N
H
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
N
N
352
S
C
N
353
N
C
N
354
N
O
N
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
N
362
N
O
N
363
N
O
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
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
N
C
N
380
N
C
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
H
N
393
N
H
N
1
N
doub
N
2
N
doub
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
sing
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
doub
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
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
doub
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
sing
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
doub
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
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
doub
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
doub
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
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
doub
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
doub
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
doub
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
sing
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
doub
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
doub
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
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
doub
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
doub
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
doub
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
doub
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
Y
144
N
sing
Y
145
N
doub
Y
146
N
doub
N
147
N
sing
Y
148
N
sing
N
149
N
sing
Y
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
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
N
161
N
sing
N
162
N
doub
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
doub
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
sing
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
doub
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
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
doub
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
Y
233
N
doub
Y
234
N
sing
Y
235
N
sing
N
236
N
sing
Y
237
N
doub
N
238
N
sing
Y
239
N
doub
N
240
N
sing
Y
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
doub
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
Y
252
N
doub
Y
253
N
sing
Y
254
N
sing
N
255
N
sing
Y
256
N
doub
N
257
N
sing
Y
258
N
sing
N
259
N
sing
Y
260
N
doub
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
doub
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
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
doub
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
sing
N
299
N
doub
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
doub
N
316
N
sing
N
317
N
sing
N
318
N
sing
N
319
N
sing
Y
320
N
doub
Y
321
N
sing
Y
322
N
sing
N
323
N
sing
Y
324
N
doub
Y
325
N
sing
Y
326
N
sing
N
327
N
sing
Y
328
N
sing
Y
329
N
doub
N
330
N
sing
Y
331
N
doub
N
332
N
sing
Y
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
sing
N
341
N
sing
N
342
N
sing
N
343
N
doub
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
sing
Y
348
N
doub
Y
349
N
sing
Y
350
N
sing
N
351
N
sing
Y
352
N
doub
N
353
N
sing
Y
354
N
doub
N
355
N
sing
Y
356
N
sing
N
357
N
sing
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
doub
N
368
N
sing
N
369
N
sing
N
370
N
sing
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
DK
J.Pept.Res.
JPERFA
2150
1397-002X
64
141
150
10.1111/j.1399-3011.2004.00181.x
15357669
Two polymorphs of a covalent complex between papain and a diazomethylketone inhibitor
2004
PL
ACTA BIOCHIM.POL.
ABPLAF
1139
0001-527X
44
601
605
Crystallization and preliminary crystallographic studies of a new crystal form of papain from Carica papaya.
1997
PL
ACTA BIOCHIM.POL.
ABPLAF
1139
0001-527X
48
1
20
Structural studies of cysteine proteases and their inhibitors
2001
US
Biochemistry
BICHAW
0033
0006-2960
15
3731
3738
Binding of chloromethyl ketone substrate analogues to crystalline papain.
1976
DK
ACTA CRYSTALLOGR.,SECT.B
ASBSDK
0622
0108-7681
48
59
66
10.1107/S0108768191006572
Structure of monoclinic papain at 1.60 Angstroms resolution
1992
NE
BIOCHIM.BIOPHYS.ACTA
BBACAQ
0113
0006-3002
1431
290
305
10.1016/S0167-4838(99)00053-9
Binding modes of a new epoxysuccinyl-peptide inhibitor of cysteine proteases. Where and how do cysteine proteases express their selectivity?
1999
10.2210/pdb1khq/pdb
pdb_00001khq
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
289
1
IMAGE PLATE
1999-04-22
MARRESEARCH
GRAPHITE
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
MACSCIENCE
23452.301
Papain
3.4.22.2
Papain, Residues 134-345
1
nat
polymer
512.001
peptidic inhibitor
1
syn
polymer
18.015
water
105
nat
water
Papaya proteinase I, PPI
no
no
IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI
HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHA
VAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN
IPEYVDWRQKGAVTPVKNQGSCGSCWAFSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGI
HYRNTYPYEGVQRYCRSREKGPYAAKTDGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHA
VAAVGYGPNYILIKNSWGTGWGENGYIRIKRGTGNSYGVCGLYTSSFYPVKN
A
polypeptide(L)
no
yes
(PHQ)LFG(0HQ)
XLFGX
I
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
papaya
Carica
sample
3649
Carica papaya
1
2.12
42
VAPOR DIFFUSION, HANGING DROP
9.2
72% methanol/ethanol (2:1), 34 mM NaCl, 50 mM 2-aminoethanol/HCl, pH 9.2, VAPOR DIFFUSION, HANGING DROP, temperature 292K
292
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_remark
pdbx_initial_refinement_model
struct_conn
repository
Initial release
Version format compliance
Atomic model
Database references
Derived calculations
Non-polymer description
Structure summary
Version format compliance
Other
Advisory
Data collection
Database references
Derived calculations
Refinement description
1
0
2003-09-09
1
1
2008-04-27
1
2
2011-07-13
1
3
2013-02-27
1
4
2023-08-16
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_remark.text
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
PAPAIN-ACETYL-ALANYL-ALANYL-PHENYLALANYL-METHYLENYLALANYL DERIVATIVE (/ACAAPACK)
PAPAIN-BENZYLOXYCARBONYL-GLYCYL-PHENYLALANYL-METHYLENYLGLYCYL DERIVATIVE (/ZGPGCK)
PAPAIN-BENZYLOXYCARBONYL-PHENYLALANYL-METHYLENYLALANYL DERIVATIVE (/ZPACK)
PAPAIN CYS 25 OXIDIZED
PAPAIN CYS 25 WITH BOUND ATOM
PAPAIN-CYSTEINYL DERIVATIVE OF CYS 25 (/PAPSSCYS)
PAPAIN COMPLEX WITH E-64-C
PAPAIN COMPLEX WITH SUCCINYL-GLN-VAL-VAL-ALA-ALA-P-NITROANILIDE
PAPAIN COMPLEX WITH E64-C (FORM II)
2-HYDROXYETHYLTHIOPAPAIN - CRYSTAL FORM D
PAPAIN COMPLEX WITH LEUPEPTIN (N-ACETYL-L-LEUCYL-L-LEUCYL-L-ARGININAL)
PAPAIN (CYS 25 CARBOXYMETHYLATED) COMPLEXED WITH THE INHIBITOR STEFIN B (CYSTATIN B) MUTANT WITH CYS I 8 REPLACED BY SER (C(I 8)S)
PAPAIN WITH CLIK148 (CATHEPSIN L SPECIFIC INHIBITOR)
MONOCLINIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX
HETEROGEN
THE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM
OF CYS 25 OF THE PROTEIN VIA A METHYLKETONE GROUP OF THE
HETGROUP GLM (-N-CH2-CO-CH2-). THE NON-STANDARD TRIPEPTIDE
IS N-TERMINALLY PROTECTED BY THE BENZYLOXYCARBONYL-
(Z- OR CBZ-) GROUP (NOT VISIBLE IN ELECTRON DENSITY).
RCSB
Y
RCSB
2001-11-30
REL
REL
HOH
water
THE PEPTIDIC INHIBITOR IS COVALENTLY LINKED TO THE SG ATOM OF CYS 25 OF THE PROTEIN VIA A METHYLKETONE GROUP. THE NON-STANDARD TRIPEPTIDE IS N-TERMINALLY PROTECTED BY THE BENZYLOXYCARBONYL-GROUP PHQ WHICH IS NOT VISIBLE IN ELECTRON DENSITY
1PPN
PDB ENTRY 1PPN
PDB
experimental model
Inhibitor
L-leucyl-N-(2-oxopropyl)-L-phenylalaninamide
Peptide-like
HOH
301
3
HOH
HOH
301
A
HOH
302
3
HOH
HOH
302
A
HOH
303
3
HOH
HOH
303
A
HOH
304
3
HOH
HOH
304
A
HOH
305
3
HOH
HOH
305
A
HOH
306
3
HOH
HOH
306
A
HOH
307
3
HOH
HOH
307
A
HOH
308
3
HOH
HOH
308
A
HOH
309
3
HOH
HOH
309
A
HOH
310
3
HOH
HOH
310
A
HOH
311
3
HOH
HOH
311
A
HOH
312
3
HOH
HOH
312
A
HOH
313
3
HOH
HOH
313
A
HOH
314
3
HOH
HOH
314
A
HOH
315
3
HOH
HOH
315
A
HOH
316
3
HOH
HOH
316
A
HOH
317
3
HOH
HOH
317
A
HOH
318
3
HOH
HOH
318
A
HOH
319
3
HOH
HOH
319
A
HOH
320
3
HOH
HOH
320
A
HOH
321
3
HOH
HOH
321
A
HOH
322
3
HOH
HOH
322
A
HOH
323
3
HOH
HOH
323
A
HOH
324
3
HOH
HOH
324
A
HOH
325
3
HOH
HOH
325
A
HOH
326
3
HOH
HOH
326
A
HOH
327
3
HOH
HOH
327
A
HOH
328
3
HOH
HOH
328
A
HOH
329
3
HOH
HOH
329
A
HOH
330
3
HOH
HOH
330
A
HOH
331
3
HOH
HOH
331
A
HOH
332
3
HOH
HOH
332
A
HOH
333
3
HOH
HOH
333
A
HOH
334
3
HOH
HOH
334
A
HOH
335
3
HOH
HOH
335
A
HOH
336
3
HOH
HOH
336
A
HOH
337
3
HOH
HOH
337
A
HOH
338
3
HOH
HOH
338
A
HOH
339
3
HOH
HOH
339
A
HOH
340
3
HOH
HOH
340
A
HOH
341
3
HOH
HOH
341
A
HOH
342
3
HOH
HOH
342
A
HOH
343
3
HOH
HOH
343
A
HOH
344
3
HOH
HOH
344
A
HOH
345
3
HOH
HOH
345
A
HOH
346
3
HOH
HOH
346
A
HOH
347
3
HOH
HOH
347
A
HOH
348
3
HOH
HOH
348
A
HOH
349
3
HOH
HOH
349
A
HOH
350
3
HOH
HOH
350
A
HOH
351
3
HOH
HOH
351
A
HOH
352
3
HOH
HOH
352
A
HOH
353
3
HOH
HOH
353
A
HOH
354
3
HOH
HOH
354
A
HOH
355
3
HOH
HOH
355
A
HOH
356
3
HOH
HOH
356
A
HOH
357
3
HOH
HOH
357
A
HOH
358
3
HOH
HOH
358
A
HOH
359
3
HOH
HOH
359
A
HOH
360
3
HOH
HOH
360
A
HOH
361
3
HOH
HOH
361
A
HOH
362
3
HOH
HOH
362
A
HOH
363
3
HOH
HOH
363
A
HOH
364
3
HOH
HOH
364
A
HOH
365
3
HOH
HOH
365
A
HOH
366
3
HOH
HOH
366
A
HOH
367
3
HOH
HOH
367
A
HOH
368
3
HOH
HOH
368
A
HOH
369
3
HOH
HOH
369
A
HOH
370
3
HOH
HOH
370
A
HOH
371
3
HOH
HOH
371
A
HOH
372
3
HOH
HOH
372
A
HOH
373
3
HOH
HOH
373
A
HOH
374
3
HOH
HOH
374
A
HOH
375
3
HOH
HOH
375
A
HOH
376
3
HOH
HOH
376
A
HOH
377
3
HOH
HOH
377
A
HOH
378
3
HOH
HOH
378
A
HOH
379
3
HOH
HOH
379
A
HOH
380
3
HOH
HOH
380
A
HOH
381
3
HOH
HOH
381
A
HOH
382
3
HOH
HOH
382
A
HOH
383
3
HOH
HOH
383
A
HOH
384
3
HOH
HOH
384
A
HOH
385
3
HOH
HOH
385
A
HOH
386
3
HOH
HOH
386
A
HOH
387
3
HOH
HOH
387
A
HOH
388
3
HOH
HOH
388
A
HOH
389
3
HOH
HOH
389
A
HOH
390
3
HOH
HOH
390
A
HOH
391
3
HOH
HOH
391
A
HOH
392
3
HOH
HOH
392
A
HOH
393
3
HOH
HOH
393
A
HOH
394
3
HOH
HOH
394
A
HOH
395
3
HOH
HOH
395
A
HOH
396
3
HOH
HOH
396
A
HOH
397
3
HOH
HOH
397
A
HOH
398
3
HOH
HOH
398
A
HOH
399
3
HOH
HOH
399
A
HOH
400
3
HOH
HOH
400
A
HOH
401
3
HOH
HOH
401
A
HOH
402
3
HOH
HOH
402
A
HOH
403
3
HOH
HOH
403
A
HOH
404
3
HOH
HOH
404
A
HOH
405
3
HOH
HOH
405
A
ILE
1
n
1
ILE
1
A
PRO
2
n
2
PRO
2
A
GLU
3
n
3
GLU
3
A
TYR
4
n
4
TYR
4
A
VAL
5
n
5
VAL
5
A
ASP
6
n
6
ASP
6
A
TRP
7
n
7
TRP
7
A
ARG
8
n
8
ARG
8
A
GLN
9
n
9
GLN
9
A
LYS
10
n
10
LYS
10
A
GLY
11
n
11
GLY
11
A
ALA
12
n
12
ALA
12
A
VAL
13
n
13
VAL
13
A
THR
14
n
14
THR
14
A
PRO
15
n
15
PRO
15
A
VAL
16
n
16
VAL
16
A
LYS
17
n
17
LYS
17
A
ASN
18
n
18
ASN
18
A
GLN
19
n
19
GLN
19
A
GLY
20
n
20
GLY
20
A
SER
21
n
21
SER
21
A
CYS
22
n
22
CYS
22
A
GLY
23
n
23
GLY
23
A
SER
24
n
24
SER
24
A
CYS
25
n
25
CYS
25
A
TRP
26
n
26
TRP
26
A
ALA
27
n
27
ALA
27
A
PHE
28
n
28
PHE
28
A
SER
29
n
29
SER
29
A
ALA
30
n
30
ALA
30
A
VAL
31
n
31
VAL
31
A
VAL
32
n
32
VAL
32
A
THR
33
n
33
THR
33
A
ILE
34
n
34
ILE
34
A
GLU
35
n
35
GLU
35
A
GLY
36
n
36
GLY
36
A
ILE
37
n
37
ILE
37
A
ILE
38
n
38
ILE
38
A
LYS
39
n
39
LYS
39
A
ILE
40
n
40
ILE
40
A
ARG
41
n
41
ARG
41
A
THR
42
n
42
THR
42
A
GLY
43
n
43
GLY
43
A
ASN
44
n
44
ASN
44
A
LEU
45
n
45
LEU
45
A
ASN
46
n
46
ASN
46
A
GLU
47
n
47
GLU
47
A
TYR
48
n
48
TYR
48
A
SER
49
n
49
SER
49
A
GLU
50
n
50
GLU
50
A
GLN
51
n
51
GLN
51
A
GLU
52
n
52
GLU
52
A
LEU
53
n
53
LEU
53
A
LEU
54
n
54
LEU
54
A
ASP
55
n
55
ASP
55
A
CYS
56
n
56
CYS
56
A
ASP
57
n
57
ASP
57
A
ARG
58
n
58
ARG
58
A
ARG
59
n
59
ARG
59
A
SER
60
n
60
SER
60
A
TYR
61
n
61
TYR
61
A
GLY
62
n
62
GLY
62
A
CYS
63
n
63
CYS
63
A
ASN
64
n
64
ASN
64
A
GLY
65
n
65
GLY
65
A
GLY
66
n
66
GLY
66
A
TYR
67
n
67
TYR
67
A
PRO
68
n
68
PRO
68
A
TRP
69
n
69
TRP
69
A
SER
70
n
70
SER
70
A
ALA
71
n
71
ALA
71
A
LEU
72
n
72
LEU
72
A
GLN
73
n
73
GLN
73
A
LEU
74
n
74
LEU
74
A
VAL
75
n
75
VAL
75
A
ALA
76
n
76
ALA
76
A
GLN
77
n
77
GLN
77
A
TYR
78
n
78
TYR
78
A
GLY
79
n
79
GLY
79
A
ILE
80
n
80
ILE
80
A
HIS
81
n
81
HIS
81
A
TYR
82
n
82
TYR
82
A
ARG
83
n
83
ARG
83
A
ASN
84
n
84
ASN
84
A
THR
85
n
85
THR
85
A
TYR
86
n
86
TYR
86
A
PRO
87
n
87
PRO
87
A
TYR
88
n
88
TYR
88
A
GLU
89
n
89
GLU
89
A
GLY
90
n
90
GLY
90
A
VAL
91
n
91
VAL
91
A
GLN
92
n
92
GLN
92
A
ARG
93
n
93
ARG
93
A
TYR
94
n
94
TYR
94
A
CYS
95
n
95
CYS
95
A
ARG
96
n
96
ARG
96
A
SER
97
n
97
SER
97
A
ARG
98
n
98
ARG
98
A
GLU
99
n
99
GLU
99
A
LYS
100
n
100
LYS
100
A
GLY
101
n
101
GLY
101
A
PRO
102
n
102
PRO
102
A
TYR
103
n
103
TYR
103
A
ALA
104
n
104
ALA
104
A
ALA
105
n
105
ALA
105
A
LYS
106
n
106
LYS
106
A
THR
107
n
107
THR
107
A
ASP
108
n
108
ASP
108
A
GLY
109
n
109
GLY
109
A
VAL
110
n
110
VAL
110
A
ARG
111
n
111
ARG
111
A
GLN
112
n
112
GLN
112
A
VAL
113
n
113
VAL
113
A
GLN
114
n
114
GLN
114
A
PRO
115
n
115
PRO
115
A
TYR
116
n
116
TYR
116
A
ASN
117
n
117
ASN
117
A
GLU
118
n
118
GLU
118
A
GLY
119
n
119
GLY
119
A
ALA
120
n
120
ALA
120
A
LEU
121
n
121
LEU
121
A
LEU
122
n
122
LEU
122
A
TYR
123
n
123
TYR
123
A
SER
124
n
124
SER
124
A
ILE
125
n
125
ILE
125
A
ALA
126
n
126
ALA
126
A
ASN
127
n
127
ASN
127
A
GLN
128
n
128
GLN
128
A
PRO
129
n
129
PRO
129
A
VAL
130
n
130
VAL
130
A
SER
131
n
131
SER
131
A
VAL
132
n
132
VAL
132
A
VAL
133
n
133
VAL
133
A
LEU
134
n
134
LEU
134
A
GLU
135
n
135
GLU
135
A
ALA
136
n
136
ALA
136
A
ALA
137
n
137
ALA
137
A
GLY
138
n
138
GLY
138
A
LYS
139
n
139
LYS
139
A
ASP
140
n
140
ASP
140
A
PHE
141
n
141
PHE
141
A
GLN
142
n
142
GLN
142
A
LEU
143
n
143
LEU
143
A
TYR
144
n
144
TYR
144
A
ARG
145
n
145
ARG
145
A
GLY
146
n
146
GLY
146
A
GLY
147
n
147
GLY
147
A
ILE
148
n
148
ILE
148
A
PHE
149
n
149
PHE
149
A
VAL
150
n
150
VAL
150
A
GLY
151
n
151
GLY
151
A
PRO
152
n
152
PRO
152
A
CYS
153
n
153
CYS
153
A
GLY
154
n
154
GLY
154
A
ASN
155
n
155
ASN
155
A
LYS
156
n
156
LYS
156
A
VAL
157
n
157
VAL
157
A
ASP
158
n
158
ASP
158
A
HIS
159
n
159
HIS
159
A
ALA
160
n
160
ALA
160
A
VAL
161
n
161
VAL
161
A
ALA
162
n
162
ALA
162
A
ALA
163
n
163
ALA
163
A
VAL
164
n
164
VAL
164
A
GLY
165
n
165
GLY
165
A
TYR
166
n
166
TYR
166
A
GLY
167
n
167
GLY
167
A
PRO
168
n
168
PRO
168
A
ASN
169
n
169
ASN
169
A
TYR
170
n
170
TYR
170
A
ILE
171
n
171
ILE
171
A
LEU
172
n
172
LEU
172
A
ILE
173
n
173
ILE
173
A
LYS
174
n
174
LYS
174
A
ASN
175
n
175
ASN
175
A
SER
176
n
176
SER
176
A
TRP
177
n
177
TRP
177
A
GLY
178
n
178
GLY
178
A
THR
179
n
179
THR
179
A
GLY
180
n
180
GLY
180
A
TRP
181
n
181
TRP
181
A
GLY
182
n
182
GLY
182
A
GLU
183
n
183
GLU
183
A
ASN
184
n
184
ASN
184
A
GLY
185
n
185
GLY
185
A
TYR
186
n
186
TYR
186
A
ILE
187
n
187
ILE
187
A
ARG
188
n
188
ARG
188
A
ILE
189
n
189
ILE
189
A
LYS
190
n
190
LYS
190
A
ARG
191
n
191
ARG
191
A
GLY
192
n
192
GLY
192
A
THR
193
n
193
THR
193
A
GLY
194
n
194
GLY
194
A
ASN
195
n
195
ASN
195
A
SER
196
n
196
SER
196
A
TYR
197
n
197
TYR
197
A
GLY
198
n
198
GLY
198
A
VAL
199
n
199
VAL
199
A
CYS
200
n
200
CYS
200
A
GLY
201
n
201
GLY
201
A
LEU
202
n
202
LEU
202
A
TYR
203
n
203
TYR
203
A
THR
204
n
204
THR
204
A
SER
205
n
205
SER
205
A
SER
206
n
206
SER
206
A
PHE
207
n
207
PHE
207
A
TYR
208
n
208
TYR
208
A
PRO
209
n
209
PRO
209
A
VAL
210
n
210
VAL
210
A
LYS
211
n
211
LYS
211
A
ASN
212
n
212
ASN
212
A
n
1
250
I
LEU
251
n
2
LEU
251
I
PHE
252
n
3
PHE
252
I
GLM
253
n
4
GLY
253
I
GLM
254
n
5
0HQ
254
I
author_and_software_defined_assembly
PISA
2
dimeric
780
-6
9480
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
130
A
N
VAL
130
A
O
ALA
163
A
O
ALA
163
A
O
TYR
166
A
O
TYR
166
A
N
VAL
5
A
N
VAL
5
A
N
VAL
130
A
N
VAL
130
A
O
ALA
163
A
O
ALA
163
A
N
ALA
162
A
N
ALA
162
A
O
LYS
174
A
O
LYS
174
A
N
ILE
173
A
N
ILE
173
A
O
ILE
187
A
O
ILE
187
A
O
ARG
188
A
O
ARG
188
A
N
PHE
149
A
N
PHE
149
A
N
ARG
111
A
N
ARG
111
A
O
TYR
208
A
O
TYR
208
1
I
PHQ
250
B
PHQ
1
1
Y
1
A
ASP
158
-151.10
7.30
14.80
-0.96
0.00
0.00
0.52
0.00
0.44
MAXIMUM LIKELIHOOD ALGORITHM. TLS PARAMETERS WERE USED. PARAMETERS WERE USED. THE CBZ (CARBOBENZOXY- OR BENZYLOXYCARBONYL-) BLOCKING GROUP AT THE N-TERMINUS OF THE INHIBITOR IS NOT VISIBLE IN ELECTRON DENSITY DUE TO DISORDER AND WAS NOT INCLUDED IN THE MODEL.
0.169
0.147
0.149
0.149
1.6
10.0
1304
24603
24603
5.0
95.1
1.91608
0.06724
RANDOM
1
THROUGHOUT
0.0
0.0
MOLECULAR REPLACEMENT
0.07936
0.07645
PDB ENTRY 1PPN
Engh & Huber
1.6
10.0
105
1784
0
0
1679
0.014
0.021
0.024
0.030
1.564
0.918
1.5
1.626
2.000
2.707
3.00
4.432
4.5
0.007
0.020
0.104
0.200
23.10
1.6
20.0
1KHQ
26000
26000
-3
-3
0.059
1
14.7
8.1
94.5
0.29
1.61
1.67
3.8
1
3.0
89.6
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
refinement
REFMAC
ORTHORHOMBIC FORM OF PAPAIN/ZLFG-DAM COVALENT COMPLEX
1
N
N
2
N
N
3
N
N
A
SER
24
A
SER
24
HELX_P
A
GLY
43
A
GLY
43
1
1
20
A
SER
49
A
SER
49
HELX_P
A
ASP
57
A
ASP
57
1
2
9
A
TYR
61
A
TYR
61
HELX_P
A
GLY
65
A
GLY
65
5
3
5
A
TYR
67
A
TYR
67
HELX_P
A
TYR
78
A
TYR
78
1
4
12
A
ASN
117
A
ASN
117
HELX_P
A
GLN
128
A
GLN
128
1
5
12
A
GLY
138
A
GLY
138
HELX_P
A
LEU
143
A
LEU
143
1
6
6
A
GLY
198
A
GLY
198
HELX_P
A
LEU
202
A
LEU
202
5
7
5
disulf
2.039
A
CYS
22
A
SG
CYS
22
1_555
A
CYS
63
A
SG
CYS
63
1_555
disulf
2.010
A
CYS
56
A
SG
CYS
56
1_555
A
CYS
95
A
SG
CYS
95
1_555
disulf
2.062
A
CYS
153
A
SG
CYS
153
1_555
A
CYS
200
A
SG
CYS
200
1_555
covale
1.804
one
A
CYS
25
A
SG
CYS
25
1_555
I
0HQ
254
B
C1
0HQ
5
1_555
covale
1.531
both
I
GLY
253
B
C
GLY
4
1_555
I
0HQ
254
B
C1
0HQ
5
1_555
HYDROLASE/HYDROLASE INHIBITOR
PROTEASE INHIBITOR, DIAZOMETHYLKETONE INHIBITOR, IRREVERSIBLE INHIBITOR, HYDROLASE-HYDROLASE INHIBITOR COMPLEX
A
GLY
151
A
GLY
151
1
A
PRO
152
A
PRO
152
0.91
PAPA_CARPA
UNP
1
1
P00784
MAMIPSISKLLFVAICLFVYMGLSFGDFSIVGYSQNDLTSTERLIQLFESWMLKHNKIYKNIDEKIYRFEIFKDNLKYID
ETNKKNNSYWLGLNVFADMSNDEFKEKYTGSIAGNYTTTELSYEEVLNDGDVNIPEYVDWRQKGAVTPVKNQGSCGSCWA
FSAVVTIEGIIKIRTGNLNEYSEQELLDCDRRSYGCNGGYPWSALQLVAQYGIHYRNTYPYEGVQRYCRSREKGPYAAKT
DGVRQVQPYNEGALLYSIANQPVSVVLEAAGKDFQLYRGGIFVGPCGNKVDHAVAAVGYGPNYILIKNSWGTGWGENGYI
RIKRGTGNSYGVCGLYTSSFYPVKN
1KHQ
PDB
2
1
1KHQ
(PHQ)LFG(OHQ)
134
345
1KHQ
1
212
P00784
A
1
1
212
250
254
1KHQ
250
254
1KHQ
I
2
1
5
3
5
2
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
A
VAL
130
A
VAL
130
A
LEU
134
A
LEU
134
A
HIS
159
A
HIS
159
A
GLY
167
A
GLY
167
A
VAL
5
A
VAL
5
A
ASP
6
A
ASP
6
A
VAL
130
A
VAL
130
A
LEU
134
A
LEU
134
A
HIS
159
A
HIS
159
A
GLY
167
A
GLY
167
A
TYR
170
A
TYR
170
A
LYS
174
A
LYS
174
A
TYR
186
A
TYR
186
A
LYS
190
A
LYS
190
A
ILE
148
A
ILE
148
A
PHE
149
A
PHE
149
A
GLY
109
A
GLY
109
A
GLN
112
A
GLN
112
A
PHE
207
A
PHE
207
A
VAL
210
A
VAL
210
BINDING SITE FOR CHAIN I OF PEPTIDIC INHIBITOR
Software
12
A
GLN
19
A
GLN
19
12
1_555
A
GLY
23
A
GLY
23
12
1_555
A
SER
24
A
SER
24
12
1_555
A
CYS
25
A
CYS
25
12
1_555
A
TRP
26
A
TRP
26
12
1_555
A
GLY
65
A
GLY
65
12
1_555
A
GLY
66
A
GLY
66
12
1_555
A
TYR
67
A
TYR
67
12
1_555
A
ARG
111
A
ARG
111
12
2_574
A
VAL
133
A
VAL
133
12
1_555
A
ASP
158
A
ASP
158
12
1_555
A
HIS
159
A
HIS
159
12
1_555
19
P 21 21 21