0.008410
0.004855
0.000000
0.000000
0.009711
0.000000
0.000000
0.000000
0.022198
0.00000
0.00000
0.00000
Yamaguchi, M.
Matoba, K.
Sawada, R.
Fujioka, Y.
Nakatogawa, H.
Yamamoto, H.
Kobashigawa, Y.
Hoshida, H.
Akada, R.
Ohsumi, Y.
Noda, N.N.
Inagaki, F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
118.908
118.908
45.050
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
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
O
N
159
N
H
N
160
N
H
N
161
N
N
N
162
S
C
N
163
N
C
N
164
N
O
N
165
S
C
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
O
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
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
N
N
184
S
C
N
185
N
C
N
186
N
O
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
O
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
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
N
N
206
S
C
N
207
N
C
N
208
N
O
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
N
N
214
N
O
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
N
N
231
S
C
N
232
N
C
N
233
N
O
N
234
N
C
N
235
N
C
N
236
N
S
N
237
N
C
N
238
N
O
N
239
N
H
N
240
N
H
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
N
N
251
S
C
N
252
N
C
N
253
N
O
N
254
N
C
Y
255
N
C
Y
256
N
C
Y
257
N
C
Y
258
N
C
Y
259
N
C
Y
260
N
C
N
261
N
O
N
262
N
H
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
N
N
274
S
C
N
275
N
C
N
276
N
O
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
O
N
281
N
H
N
282
N
H
N
283
N
H
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
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
N
C
N
295
N
O
N
296
N
O
N
297
N
H
N
298
N
H
N
299
N
H
N
300
N
H
N
301
N
H
N
302
N
H
N
303
N
H
N
304
N
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
R
C
N
309
N
O
N
310
N
C
N
311
N
O
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
N
Y
330
N
C
Y
331
N
C
Y
332
N
C
Y
333
N
C
Y
334
N
C
N
335
N
O
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
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
N
N
349
S
C
N
350
N
C
N
351
N
O
N
352
N
C
Y
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
N
359
N
O
N
360
N
O
N
361
N
H
N
362
N
H
N
363
N
H
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
N
N
373
S
C
N
374
N
C
N
375
N
O
N
376
N
C
N
377
N
C
N
378
N
C
N
379
N
O
N
380
N
H
N
381
N
H
N
382
N
H
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
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
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
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
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
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
doub
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
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
doub
N
225
N
sing
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
sing
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
doub
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
Y
248
N
doub
Y
249
N
sing
Y
250
N
sing
N
251
N
sing
Y
252
N
doub
N
253
N
sing
Y
254
N
doub
N
255
N
sing
Y
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
doub
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
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
doub
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
doub
N
297
N
sing
N
298
N
sing
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
doub
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
Y
317
N
doub
Y
318
N
sing
Y
319
N
sing
N
320
N
sing
Y
321
N
doub
Y
322
N
sing
Y
323
N
sing
N
324
N
sing
Y
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
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
N
350
N
sing
Y
351
N
doub
N
352
N
sing
Y
353
N
sing
N
354
N
sing
N
355
N
sing
N
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
doub
N
365
N
sing
N
366
N
sing
N
367
N
sing
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
US
Nat.Struct.Mol.Biol.
1545-9985
19
1250
1256
10.1038/nsmb.2451
23142983
Noncanonical recognition and UBL loading of distinct E2s by autophagy-essential Atg7.
2012
10.2210/pdb3vx6/pdb
pdb_00003vx6
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100
1
CCD
2011-01-24
RAYONIX MX225HE
Rotated-inclined double-crystal monochromator , Si (111)
SINGLE WAVELENGTH
M
x-ray
1
1.0000
1.0
BL41XU
SPring-8
1.0000
SYNCHROTRON
SPRING-8 BEAMLINE BL41XU
32213.869
E1
1
man
polymer
18.015
water
17
nat
water
no
no
GPHMMVSDLKFAPSFQSFVDSSFFHELSRLKLDIFKLDSDEKALYTQLDLNQFTSNVLAISLRDDSFQKPDNDEHNIILK
GYLLNFNTIELFKNCNKIQFIKEKGQELLQRGLENDLNEIISFYMISFADLKKYKFYYWICMPSFQSDGATYQIISSKVI
ASDSDISVSFIKQNVIIACVISGVIQKATPDNLKVCEKVVFKDFSHLKDIPSAVTKNILTVWSKLSPRETYTICFLRSDE
SSFEAEIIINNGNNPSLKVSGWEKNGLGKLAPKSIDLSSLMDP
GPHMMVSDLKFAPSFQSFVDSSFFHELSRLKLDIFKLDSDEKALYTQLDLNQFTSNVLAISLRDDSFQKPDNDEHNIILK
GYLLNFNTIELFKNCNKIQFIKEKGQELLQRGLENDLNEIISFYMISFADLKKYKFYYWICMPSFQSDGATYQIISSKVI
ASDSDISVSFIKQNVIIACVISGVIQKATPDNLKVCEKVVFKDFSHLKDIPSAVTKNILTVWSKLSPRETYTICFLRSDE
SSFEAEIIINNGNNPSLKVSGWEKNGLGKLAPKSIDLSSLMDP
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
sample
4911
Kluyveromyces marxianus
562
Escherichia coli
BL21 DE3
PLASMID
pGBHPS
1
2.85
56.90
VAPOR DIFFUSION, SITTING DROP
5.6
2.0M ammonium sulfate, 0.2M potassium/sodium tartrate, 0.1M citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
chem_comp_atom
chem_comp_bond
citation
database_2
pdbx_initial_refinement_model
repository
Initial release
Data collection
Database references
Refinement description
1
0
2012-11-14
1
1
2023-10-18
1
2
2023-11-08
_citation.country
_citation.journal_abbrev
_citation.journal_id_CSD
_citation.journal_id_ISSN
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.pdbx_database_id_DOI
_citation.pdbx_database_id_PubMed
_citation.title
_citation.year
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
PDBJ
Y
PDBJ
2012-09-11
REL
REL
HOH
water
A SEQUENCE DATABASE REFERENCE FOR THIS PROTEIN DOES NOT CURRENTLY EXIST.
3VH1
PDB ENTRY 3VH1
PDB
experimental model
HOH
1
2
HOH
HOH
301
A
HOH
2
2
HOH
HOH
302
A
HOH
3
2
HOH
HOH
303
A
HOH
4
2
HOH
HOH
304
A
HOH
5
2
HOH
HOH
305
A
HOH
6
2
HOH
HOH
306
A
HOH
7
2
HOH
HOH
307
A
HOH
8
2
HOH
HOH
308
A
HOH
9
2
HOH
HOH
309
A
HOH
10
2
HOH
HOH
310
A
HOH
11
2
HOH
HOH
311
A
HOH
12
2
HOH
HOH
312
A
HOH
13
2
HOH
HOH
313
A
HOH
14
2
HOH
HOH
314
A
HOH
15
2
HOH
HOH
315
A
HOH
16
2
HOH
HOH
316
A
HOH
17
2
HOH
HOH
317
A
n
1
-3
A
n
2
-2
A
n
3
-1
A
n
4
0
A
n
5
1
A
n
6
2
A
n
7
3
A
ASP
4
n
8
ASP
4
A
LEU
5
n
9
LEU
5
A
LYS
6
n
10
LYS
6
A
PHE
7
n
11
PHE
7
A
ALA
8
n
12
ALA
8
A
PRO
9
n
13
PRO
9
A
SER
10
n
14
SER
10
A
PHE
11
n
15
PHE
11
A
GLN
12
n
16
GLN
12
A
SER
13
n
17
SER
13
A
PHE
14
n
18
PHE
14
A
VAL
15
n
19
VAL
15
A
ASP
16
n
20
ASP
16
A
SER
17
n
21
SER
17
A
SER
18
n
22
SER
18
A
PHE
19
n
23
PHE
19
A
PHE
20
n
24
PHE
20
A
HIS
21
n
25
HIS
21
A
GLU
22
n
26
GLU
22
A
LEU
23
n
27
LEU
23
A
SER
24
n
28
SER
24
A
ARG
25
n
29
ARG
25
A
LEU
26
n
30
LEU
26
A
LYS
27
n
31
LYS
27
A
LEU
28
n
32
LEU
28
A
ASP
29
n
33
ASP
29
A
ILE
30
n
34
ILE
30
A
PHE
31
n
35
PHE
31
A
LYS
32
n
36
LYS
32
A
LEU
33
n
37
LEU
33
A
ASP
34
n
38
ASP
34
A
SER
35
n
39
SER
35
A
ASP
36
n
40
ASP
36
A
GLU
37
n
41
GLU
37
A
LYS
38
n
42
LYS
38
A
ALA
39
n
43
ALA
39
A
LEU
40
n
44
LEU
40
A
TYR
41
n
45
TYR
41
A
THR
42
n
46
THR
42
A
GLN
43
n
47
GLN
43
A
LEU
44
n
48
LEU
44
A
ASP
45
n
49
ASP
45
A
LEU
46
n
50
LEU
46
A
ASN
47
n
51
ASN
47
A
GLN
48
n
52
GLN
48
A
PHE
49
n
53
PHE
49
A
THR
50
n
54
THR
50
A
SER
51
n
55
SER
51
A
ASN
52
n
56
ASN
52
A
VAL
53
n
57
VAL
53
A
LEU
54
n
58
LEU
54
A
ALA
55
n
59
ALA
55
A
ILE
56
n
60
ILE
56
A
SER
57
n
61
SER
57
A
LEU
58
n
62
LEU
58
A
ARG
59
n
63
ARG
59
A
ASP
60
n
64
ASP
60
A
ASP
61
n
65
ASP
61
A
SER
62
n
66
SER
62
A
PHE
63
n
67
PHE
63
A
GLN
64
n
68
GLN
64
A
LYS
65
n
69
LYS
65
A
PRO
66
n
70
PRO
66
A
ASP
67
n
71
ASP
67
A
n
72
68
A
n
73
69
A
n
74
70
A
HIS
71
n
75
HIS
71
A
ASN
72
n
76
ASN
72
A
ILE
73
n
77
ILE
73
A
ILE
74
n
78
ILE
74
A
LEU
75
n
79
LEU
75
A
LYS
76
n
80
LYS
76
A
GLY
77
n
81
GLY
77
A
TYR
78
n
82
TYR
78
A
LEU
79
n
83
LEU
79
A
LEU
80
n
84
LEU
80
A
ASN
81
n
85
ASN
81
A
PHE
82
n
86
PHE
82
A
ASN
83
n
87
ASN
83
A
THR
84
n
88
THR
84
A
ILE
85
n
89
ILE
85
A
GLU
86
n
90
GLU
86
A
LEU
87
n
91
LEU
87
A
PHE
88
n
92
PHE
88
A
LYS
89
n
93
LYS
89
A
ASN
90
n
94
ASN
90
A
CYS
91
n
95
CYS
91
A
ASN
92
n
96
ASN
92
A
LYS
93
n
97
LYS
93
A
ILE
94
n
98
ILE
94
A
GLN
95
n
99
GLN
95
A
PHE
96
n
100
PHE
96
A
ILE
97
n
101
ILE
97
A
LYS
98
n
102
LYS
98
A
GLU
99
n
103
GLU
99
A
LYS
100
n
104
LYS
100
A
GLY
101
n
105
GLY
101
A
GLN
102
n
106
GLN
102
A
GLU
103
n
107
GLU
103
A
LEU
104
n
108
LEU
104
A
LEU
105
n
109
LEU
105
A
GLN
106
n
110
GLN
106
A
ARG
107
n
111
ARG
107
A
GLY
108
n
112
GLY
108
A
LEU
109
n
113
LEU
109
A
GLU
110
n
114
GLU
110
A
ASN
111
n
115
ASN
111
A
ASP
112
n
116
ASP
112
A
LEU
113
n
117
LEU
113
A
ASN
114
n
118
ASN
114
A
GLU
115
n
119
GLU
115
A
ILE
116
n
120
ILE
116
A
ILE
117
n
121
ILE
117
A
SER
118
n
122
SER
118
A
PHE
119
n
123
PHE
119
A
TYR
120
n
124
TYR
120
A
MET
121
n
125
MET
121
A
ILE
122
n
126
ILE
122
A
SER
123
n
127
SER
123
A
PHE
124
n
128
PHE
124
A
ALA
125
n
129
ALA
125
A
ASP
126
n
130
ASP
126
A
LEU
127
n
131
LEU
127
A
LYS
128
n
132
LYS
128
A
LYS
129
n
133
LYS
129
A
TYR
130
n
134
TYR
130
A
LYS
131
n
135
LYS
131
A
PHE
132
n
136
PHE
132
A
TYR
133
n
137
TYR
133
A
TYR
134
n
138
TYR
134
A
TRP
135
n
139
TRP
135
A
ILE
136
n
140
ILE
136
A
CYS
137
n
141
CYS
137
A
MET
138
n
142
MET
138
A
PRO
139
n
143
PRO
139
A
SER
140
n
144
SER
140
A
PHE
141
n
145
PHE
141
A
GLN
142
n
146
GLN
142
A
SER
143
n
147
SER
143
A
ASP
144
n
148
ASP
144
A
GLY
145
n
149
GLY
145
A
ALA
146
n
150
ALA
146
A
THR
147
n
151
THR
147
A
TYR
148
n
152
TYR
148
A
GLN
149
n
153
GLN
149
A
ILE
150
n
154
ILE
150
A
ILE
151
n
155
ILE
151
A
SER
152
n
156
SER
152
A
SER
153
n
157
SER
153
A
LYS
154
n
158
LYS
154
A
VAL
155
n
159
VAL
155
A
ILE
156
n
160
ILE
156
A
ALA
157
n
161
ALA
157
A
SER
158
n
162
SER
158
A
ASP
159
n
163
ASP
159
A
SER
160
n
164
SER
160
A
ASP
161
n
165
ASP
161
A
ILE
162
n
166
ILE
162
A
SER
163
n
167
SER
163
A
VAL
164
n
168
VAL
164
A
SER
165
n
169
SER
165
A
PHE
166
n
170
PHE
166
A
ILE
167
n
171
ILE
167
A
LYS
168
n
172
LYS
168
A
GLN
169
n
173
GLN
169
A
ASN
170
n
174
ASN
170
A
VAL
171
n
175
VAL
171
A
ILE
172
n
176
ILE
172
A
ILE
173
n
177
ILE
173
A
ALA
174
n
178
ALA
174
A
CYS
175
n
179
CYS
175
A
VAL
176
n
180
VAL
176
A
ILE
177
n
181
ILE
177
A
SER
178
n
182
SER
178
A
GLY
179
n
183
GLY
179
A
VAL
180
n
184
VAL
180
A
ILE
181
n
185
ILE
181
A
GLN
182
n
186
GLN
182
A
LYS
183
n
187
LYS
183
A
ALA
184
n
188
ALA
184
A
THR
185
n
189
THR
185
A
PRO
186
n
190
PRO
186
A
ASP
187
n
191
ASP
187
A
ASN
188
n
192
ASN
188
A
LEU
189
n
193
LEU
189
A
LYS
190
n
194
LYS
190
A
VAL
191
n
195
VAL
191
A
CYS
192
n
196
CYS
192
A
GLU
193
n
197
GLU
193
A
LYS
194
n
198
LYS
194
A
VAL
195
n
199
VAL
195
A
VAL
196
n
200
VAL
196
A
PHE
197
n
201
PHE
197
A
LYS
198
n
202
LYS
198
A
ASP
199
n
203
ASP
199
A
PHE
200
n
204
PHE
200
A
SER
201
n
205
SER
201
A
HIS
202
n
206
HIS
202
A
LEU
203
n
207
LEU
203
A
LYS
204
n
208
LYS
204
A
ASP
205
n
209
ASP
205
A
ILE
206
n
210
ILE
206
A
PRO
207
n
211
PRO
207
A
SER
208
n
212
SER
208
A
ALA
209
n
213
ALA
209
A
VAL
210
n
214
VAL
210
A
THR
211
n
215
THR
211
A
LYS
212
n
216
LYS
212
A
ASN
213
n
217
ASN
213
A
ILE
214
n
218
ILE
214
A
LEU
215
n
219
LEU
215
A
THR
216
n
220
THR
216
A
VAL
217
n
221
VAL
217
A
TRP
218
n
222
TRP
218
A
SER
219
n
223
SER
219
A
LYS
220
n
224
LYS
220
A
LEU
221
n
225
LEU
221
A
SER
222
n
226
SER
222
A
PRO
223
n
227
PRO
223
A
ARG
224
n
228
ARG
224
A
GLU
225
n
229
GLU
225
A
THR
226
n
230
THR
226
A
TYR
227
n
231
TYR
227
A
THR
228
n
232
THR
228
A
ILE
229
n
233
ILE
229
A
CYS
230
n
234
CYS
230
A
PHE
231
n
235
PHE
231
A
LEU
232
n
236
LEU
232
A
ARG
233
n
237
ARG
233
A
SER
234
n
238
SER
234
A
ASP
235
n
239
ASP
235
A
GLU
236
n
240
GLU
236
A
SER
237
n
241
SER
237
A
SER
238
n
242
SER
238
A
PHE
239
n
243
PHE
239
A
GLU
240
n
244
GLU
240
A
ALA
241
n
245
ALA
241
A
GLU
242
n
246
GLU
242
A
ILE
243
n
247
ILE
243
A
ILE
244
n
248
ILE
244
A
ILE
245
n
249
ILE
245
A
ASN
246
n
250
ASN
246
A
ASN
247
n
251
ASN
247
A
GLY
248
n
252
GLY
248
A
ASN
249
n
253
ASN
249
A
ASN
250
n
254
ASN
250
A
PRO
251
n
255
PRO
251
A
SER
252
n
256
SER
252
A
LEU
253
n
257
LEU
253
A
LYS
254
n
258
LYS
254
A
VAL
255
n
259
VAL
255
A
SER
256
n
260
SER
256
A
GLY
257
n
261
GLY
257
A
TRP
258
n
262
TRP
258
A
GLU
259
n
263
GLU
259
A
LYS
260
n
264
LYS
260
A
n
265
261
A
n
266
262
A
n
267
263
A
n
268
264
A
n
269
265
A
LEU
266
n
270
LEU
266
A
ALA
267
n
271
ALA
267
A
PRO
268
n
272
PRO
268
A
LYS
269
n
273
LYS
269
A
SER
270
n
274
SER
270
A
ILE
271
n
275
ILE
271
A
ASP
272
n
276
ASP
272
A
LEU
273
n
277
LEU
273
A
SER
274
n
278
SER
274
A
SER
275
n
279
SER
275
A
LEU
276
n
280
LEU
276
A
n
281
277
A
n
282
278
A
n
283
279
A
author_defined_assembly
1
monomeric
software_defined_assembly
PISA
2
dimeric
1320
-9
23580
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
-0.5000000000
-0.8660254038
0.0000000000
-0.8660254038
0.5000000000
0.0000000000
0.0000000000
0.0000000000
-1.0000000000
6_554
-x,-x+y,-z-2/3
crystal symmetry operation
0.0000000000
0.0000000000
-30.0333333333
A
N
PHE
14
A
N
PHE
18
A
O
LEU
58
A
O
LEU
62
A
N
LYS
38
A
N
LYS
42
A
O
LEU
79
A
O
LEU
83
A
N
LEU
80
A
N
LEU
84
A
O
MET
121
A
O
MET
125
A
N
PHE
124
A
N
PHE
128
A
O
TYR
133
A
O
TYR
137
A
N
SER
140
A
N
SER
144
A
O
SER
256
A
O
SER
260
A
N
LYS
38
A
N
LYS
42
A
O
LEU
79
A
O
LEU
83
A
N
LEU
80
A
N
LEU
84
A
O
MET
121
A
O
MET
125
A
N
PHE
124
A
N
PHE
128
A
O
TYR
133
A
O
TYR
137
A
N
TYR
134
A
N
TYR
138
A
O
LYS
269
A
O
LYS
273
A
N
SER
152
A
N
SER
156
A
O
GLU
242
A
O
GLU
246
A
O
ILE
243
A
O
ILE
247
A
N
TYR
227
A
N
TYR
231
A
O
CYS
230
A
O
CYS
234
A
N
PHE
197
A
N
PHE
201
A
O
VAL
196
A
O
VAL
200
A
N
ALA
174
A
N
ALA
178
A
N
CYS
175
A
N
CYS
179
A
O
GLN
182
A
O
GLN
186
1
A
CG
PHE
31
A
CG
PHE
35
1
Y
1
A
CD1
PHE
31
A
CD1
PHE
35
1
Y
1
A
CD2
PHE
31
A
CD2
PHE
35
1
Y
1
A
CE1
PHE
31
A
CE1
PHE
35
1
Y
1
A
CE2
PHE
31
A
CE2
PHE
35
1
Y
1
A
CZ
PHE
31
A
CZ
PHE
35
1
Y
1
A
CG
LYS
32
A
CG
LYS
36
1
Y
1
A
CD
LYS
32
A
CD
LYS
36
1
Y
1
A
CE
LYS
32
A
CE
LYS
36
1
Y
1
A
NZ
LYS
32
A
NZ
LYS
36
1
Y
1
A
CG
LYS
168
A
CG
LYS
172
1
Y
1
A
CD
LYS
168
A
CD
LYS
172
1
Y
1
A
CE
LYS
168
A
CE
LYS
172
1
Y
1
A
NZ
LYS
168
A
NZ
LYS
172
1
Y
1
A
CG
LYS
204
A
CG
LYS
208
1
Y
1
A
CD
LYS
204
A
CD
LYS
208
1
Y
1
A
CE
LYS
204
A
CE
LYS
208
1
Y
1
A
NZ
LYS
204
A
NZ
LYS
208
1
Y
1
A
CG
LYS
260
A
CG
LYS
264
1
Y
1
A
CD
LYS
260
A
CD
LYS
264
1
Y
1
A
CE
LYS
260
A
CE
LYS
264
1
Y
1
A
NZ
LYS
260
A
NZ
LYS
264
1
Y
1
A
GLY
-3
A
GLY
1
1
Y
1
A
PRO
-2
A
PRO
2
1
Y
1
A
HIS
-1
A
HIS
3
1
Y
1
A
MET
0
A
MET
4
1
Y
1
A
MET
1
A
MET
5
1
Y
1
A
VAL
2
A
VAL
6
1
Y
1
A
SER
3
A
SER
7
1
Y
1
A
ASN
68
A
ASN
72
1
Y
1
A
ASP
69
A
ASP
73
1
Y
1
A
GLU
70
A
GLU
74
1
Y
1
A
ASN
261
A
ASN
265
1
Y
1
A
GLY
262
A
GLY
266
1
Y
1
A
LEU
263
A
LEU
267
1
Y
1
A
GLY
264
A
GLY
268
1
Y
1
A
LYS
265
A
LYS
269
1
Y
1
A
MET
277
A
MET
281
1
Y
1
A
ASP
278
A
ASP
282
1
Y
1
A
PRO
279
A
PRO
283
1
Y
1
A
PHE
31
-64.98
70.11
1
A
ASN
47
-91.86
-65.53
1
A
ASN
52
68.90
-5.97
1
A
ARG
59
-110.07
-161.59
1
A
SER
62
-55.13
-3.88
1
A
ASN
92
-65.83
86.89
1
A
ASN
111
-129.30
-79.94
1
A
LYS
128
-90.83
-76.22
1
A
ASP
205
56.34
11.38
1
A
GLU
236
91.03
-8.06
1
A
SER
274
-158.12
44.92
protein_rep.param
protein.top
dna-rna_rep.param
dna-rna.top
water_rep.param
water.top
ion.param
ion.top
carbohydrate.param
carbohydrate.top
49.7
4.98
0.00
0.00
4.98
0.00
-9.97
BULK SOLVENT MODEL USED
0.268
0.008
0.224
0.228
0.224
2.60
38.92
1168
11354
10.3
98.8
RANDOM
97156.18
0.000000
1
RESTRAINED
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
PDB ENTRY 3VH1
Engh & Huber
FLAT MODEL
31.4125
0.38
0.44
0.34
5.00
0.52
0.39
2.60
38.92
17
2130
0
0
2113
0.009
1.5
24.7
0.86
1.27
1.50
2.17
2.00
1.77
2.00
2.72
2.50
0.347
0.025
0.303
2.76
193
1600
1793
6
10.8
94.4
62.1
2.60
38.92
3VX6
12559
12144
0
-3
0.065
1
19.2
20.0
96.7
2.60
2.69
8.6
1251
0.300
1
19.6
67.0
data collection
HKL-2000
phasing
MOLREP
refinement
CNS
1.3
data reduction
HKL-2000
data scaling
HKL-2000
Crystal structure of Kluyveromyces marxianus Atg7NTD
1
N
N
2
N
N
A
ASP
16
A
ASP
20
HELX_P
A
ILE
30
A
ILE
34
1
1
15
A
ARG
59
A
ARG
63
HELX_P
A
GLN
64
A
GLN
68
5
2
6
A
THR
84
A
THR
88
HELX_P
A
CYS
91
A
CYS
95
1
3
8
A
ASN
92
A
ASN
96
HELX_P
A
ASN
111
A
ASN
115
1
4
20
A
ASP
112
A
ASP
116
HELX_P
A
ILE
117
A
ILE
121
5
5
6
A
SER
160
A
SER
164
HELX_P
A
LYS
168
A
LYS
172
1
6
9
A
THR
185
A
THR
189
HELX_P
A
CYS
192
A
CYS
196
1
7
8
A
VAL
210
A
VAL
214
HELX_P
A
SER
222
A
SER
226
1
8
13
LIGASE
E2 binding, E1, Ligase
3VX6
PDB
1
3VX6
-3
279
3VX6
-3
279
3VX6
A
1
1
283
2
5
5
6
parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
A
GLN
12
A
GLN
16
A
VAL
15
A
VAL
19
A
ALA
55
A
ALA
59
A
LEU
58
A
LEU
62
A
ASP
36
A
ASP
40
A
GLN
43
A
GLN
47
A
ILE
74
A
ILE
78
A
PHE
82
A
PHE
86
A
PHE
119
A
PHE
123
A
ASP
126
A
ASP
130
A
LYS
131
A
LYS
135
A
SER
140
A
SER
144
A
SER
256
A
SER
260
A
TRP
258
A
TRP
262
A
ASP
36
A
ASP
40
A
GLN
43
A
GLN
47
A
ILE
74
A
ILE
78
A
PHE
82
A
PHE
86
A
PHE
119
A
PHE
123
A
ASP
126
A
ASP
130
A
LYS
131
A
LYS
135
A
SER
140
A
SER
144
A
LYS
269
A
LYS
273
A
ILE
271
A
ILE
275
A
THR
147
A
THR
151
A
VAL
155
A
VAL
159
A
PHE
239
A
PHE
243
A
ASN
246
A
ASN
250
A
TYR
227
A
TYR
231
A
LEU
232
A
LEU
236
A
LYS
194
A
LYS
198
A
LYS
198
A
LYS
202
A
ILE
173
A
ILE
177
A
ILE
177
A
ILE
181
A
VAL
180
A
VAL
184
A
GLN
182
A
GLN
186
152
P 31 2 1