0.028286
0.000000
0.000000
0.000000
0.014575
0.000000
0.000000
0.000000
0.011036
0.00000
0.00000
0.00000
Companon, I.
Castro-Lopez, J.
Escudero-Casao, M.
Avenoza, A.
Busto, J.H.
Castillon, S.
Jimenez-Barbero, J.
Bernardes, G.J.
Boutureira, O.
Jimenez-Oses, G.
Asensio, J.L.
Peregrina, J.M.
0000-0002-3122-9401
Hurtado-Guerrero, R.
Corzana, F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
35.353
68.612
90.609
C8 H15 N O6
221.208
2-acetamido-2-deoxy-alpha-D-galactopyranose
N-acetyl-alpha-D-galactosamine; 2-acetamido-2-deoxy-alpha-D-galactose; 2-acetamido-2-deoxy-D-galactose; 2-acetamido-2-deoxy-galactose; N-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
D-saccharide, alpha linking
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
C2 H6 O2
62.068
1,2-ETHANEDIOL
ETHYLENE GLYCOL
non-polymer
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
H2 N
16.023
AMINO GROUP
non-polymer
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 O2 Se
182.080
n
Selenothreonine
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
O
N
2
S
C
N
3
N
O
N
4
R
C
N
5
N
N
N
6
R
C
N
7
N
O
N
8
R
C
N
9
N
O
N
10
R
C
N
11
N
C
N
12
N
O
N
13
N
C
N
14
N
O
N
15
N
C
N
16
N
H
N
17
N
H
N
18
N
H
N
19
N
H
N
20
N
H
N
21
N
H
N
22
N
H
N
23
N
H
N
24
N
H
N
25
N
H
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
N
N
32
S
C
N
33
N
C
N
34
N
O
N
35
N
C
N
36
N
O
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
N
N
45
S
C
N
46
N
C
N
47
N
O
N
48
N
C
N
49
N
C
N
50
N
C
N
51
N
N
N
52
N
C
N
53
N
N
N
54
N
N
N
55
N
O
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
H
N
64
N
H
N
65
N
H
N
66
N
H
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
N
N
72
S
C
N
73
N
C
N
74
N
O
N
75
N
C
N
76
N
C
N
77
N
O
N
78
N
N
N
79
N
O
N
80
N
H
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
O
N
95
N
O
N
96
N
O
N
97
N
H
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
N
N
105
R
C
N
106
N
C
N
107
N
O
N
108
N
C
N
109
N
S
N
110
N
O
N
111
N
H
N
112
N
H
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
C
N
119
N
O
N
120
N
C
N
121
N
O
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
N
N
129
S
C
N
130
N
C
N
131
N
O
N
132
N
C
N
133
N
C
N
134
N
C
N
135
N
O
N
136
N
N
N
137
N
O
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
N
N
149
S
C
N
150
N
C
N
151
N
O
N
152
N
C
N
153
N
C
N
154
N
C
N
155
N
O
N
156
N
O
N
157
N
O
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
N
N
168
N
C
N
169
N
C
N
170
N
O
N
171
N
O
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
N
N
178
S
C
N
179
N
C
N
180
N
O
N
181
N
C
Y
182
N
C
Y
183
N
N
Y
184
N
C
Y
185
N
C
Y
186
N
N
N
187
N
O
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
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
O
N
199
N
H
N
200
N
H
N
201
N
N
N
202
S
C
N
203
N
C
N
204
N
O
N
205
S
C
N
206
N
C
N
207
N
C
N
208
N
C
N
209
N
O
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
N
N
224
S
C
N
225
N
C
N
226
N
O
N
227
N
C
N
228
N
C
N
229
N
C
N
230
N
C
N
231
N
O
N
232
N
H
N
233
N
H
N
234
N
H
N
235
N
H
N
236
N
H
N
237
N
H
N
238
N
H
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
N
N
246
S
C
N
247
N
C
N
248
N
O
N
249
N
C
N
250
N
C
N
251
N
C
N
252
N
C
N
253
N
N
N
254
N
O
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
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
N
N
271
S
C
N
272
N
C
N
273
N
O
N
274
N
C
N
275
N
C
N
276
N
S
N
277
N
C
N
278
N
O
N
279
N
H
N
280
N
H
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
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
Y
298
N
C
Y
299
N
C
Y
300
N
C
Y
301
N
C
Y
302
N
C
Y
303
N
C
N
304
N
O
N
305
N
H
N
306
N
H
N
307
N
H
N
308
N
H
N
309
N
H
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
N
N
317
S
C
N
318
N
C
N
319
N
O
N
320
N
C
N
321
N
C
N
322
N
C
N
323
N
O
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
H
N
333
N
N
N
334
S
C
N
335
N
C
N
336
N
O
N
337
N
C
N
338
N
O
N
339
N
O
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
N
N
348
R
C
N
349
R
C
N
350
N
C
N
351
N
SE
N
352
N
C
N
353
N
O
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
H
N
362
N
O
N
363
N
H
N
364
N
N
N
365
S
C
N
366
N
C
N
367
N
O
N
368
R
C
N
369
N
O
N
370
N
C
N
371
N
O
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
N
H
N
380
N
H
N
381
N
N
N
382
S
C
N
383
N
C
N
384
N
O
N
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
N
Y
390
N
C
Y
391
N
C
Y
392
N
C
Y
393
N
C
Y
394
N
C
N
395
N
O
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
H
N
405
N
H
N
406
N
H
N
407
N
H
N
408
N
N
N
409
S
C
N
410
N
C
N
411
N
O
N
412
N
C
Y
413
N
C
Y
414
N
C
Y
415
N
C
Y
416
N
C
Y
417
N
C
Y
418
N
C
N
419
N
O
N
420
N
O
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
N
N
433
S
C
N
434
N
C
N
435
N
O
N
436
N
C
N
437
N
C
N
438
N
C
N
439
N
O
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
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
sing
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
sing
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
doub
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
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
sing
N
62
N
sing
N
63
N
doub
N
64
N
sing
N
65
N
sing
N
66
N
sing
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
doub
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
doub
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
doub
N
97
N
sing
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
doub
N
107
N
sing
N
108
N
sing
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
sing
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
sing
N
127
N
sing
N
128
N
doub
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
sing
N
136
N
doub
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
doub
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
doub
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
sing
N
163
N
sing
N
164
N
sing
N
165
N
doub
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
doub
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
Y
179
N
sing
Y
180
N
doub
Y
181
N
doub
N
182
N
sing
Y
183
N
sing
N
184
N
sing
Y
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
doub
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
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
doub
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
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
doub
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
sing
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
doub
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
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
doub
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
Y
289
N
doub
Y
290
N
sing
Y
291
N
sing
N
292
N
sing
Y
293
N
doub
N
294
N
sing
Y
295
N
doub
N
296
N
sing
Y
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
doub
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
sing
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
doub
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
doub
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
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
doub
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
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
doub
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
Y
374
N
doub
Y
375
N
sing
Y
376
N
sing
N
377
N
sing
Y
378
N
doub
Y
379
N
sing
Y
380
N
sing
N
381
N
sing
Y
382
N
sing
Y
383
N
doub
N
384
N
sing
Y
385
N
doub
N
386
N
sing
Y
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
doub
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
Y
402
N
doub
Y
403
N
sing
Y
404
N
sing
N
405
N
sing
Y
406
N
doub
N
407
N
sing
Y
408
N
doub
N
409
N
sing
Y
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
N
414
N
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
sing
N
421
N
doub
N
422
N
sing
N
423
N
sing
N
424
N
sing
N
425
N
sing
N
426
N
sing
N
427
N
sing
N
428
N
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
sing
US
J. Am. Chem. Soc.
JACSAT
1520-5126
141
4063
4072
10.1021/jacs.8b13503
30726084
Structure-Based Design of Potent Tumor-Associated Antigens: Modulation of Peptide Presentation by Single-Atom O/S or O/Se Substitutions at the Glycosidic Linkage.
2019
10.2210/pdb6frj/pdb
pdb_00006frj
100
1
PIXEL
2017-12-15
DECTRIS PILATUS3 S 6M
SINGLE WAVELENGTH
M
x-ray
1
0.979
1.0
XALOC
ALBA
0.979
SYNCHROTRON
ALBA BEAMLINE XALOC
Although this structure is a ScFv, please follow the same numbering as shown in PDB entry 5OWP.
25758.338
scFv-SM3
1
man
polymer
717.677
APD-SeThr-RP
1
syn
polymer
62.068
1,2-ETHANEDIOL
4
syn
non-polymer
221.208
2-acetamido-2-deoxy-alpha-D-galactopyranose
1
man
non-polymer
18.015
water
163
nat
water
no
no
QVQLQESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYATHYAESVKGRFTISRDDSKSS
VYLQMNNLRAEDTGIYYCTGVGQFAYWGQGTTVTVSSSSGGGGSGGGGGSSGSSDIVVTQESALTTSPGETVTLTCRSST
GAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKL
TVLG
QVQLQESGGGLVQPGGSMKLSCVASGFTFSNYWMNWVRQSPEKGLEWVAEIRLKSNNYATHYAESVKGRFTISRDDSKSS
VYLQMNNLRAEDTGIYYCTGVGQFAYWGQGTTVTVSSSSGGGGSGGGGGSSGSSDIVVTQESALTTSPGETVTLTCRSST
GAVTTSNYANWVQEKPDHLFTGLIGGTNNRAPGVPARFSGSLIGDKAALTITGAQTEDEAIYFCALWYSNHWVFGGGTKL
TVLG
H
polypeptide(L)
no
yes
APD(T9E)RP(NH2)
APDTRPX
B
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
sample
1
244
10090
Mus musculus
4922
Komagataella pastoris
Biological sequence
1
2.06
40.34
VAPOR DIFFUSION, SITTING DROP
PEG 3350
disodium hydrogen phosphate
291
pdbx_data_processing_status
pdbx_validate_symm_contact
struct_conn
citation
database_PDB_rev
database_PDB_rev_record
pdbx_database_proc
atom_site
chem_comp
entity
pdbx_chem_comp_identifier
pdbx_entity_nonpoly
struct_conn
struct_site
struct_site_gen
chem_comp
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
struct_conn
repository
Initial release
Carbohydrate remediation
repository
Remediation
Advisory
Data collection
Derived calculations
Data collection
Database references
Atomic model
Data collection
Derived calculations
Structure summary
Data collection
Database references
Derived calculations
Refinement description
Structure summary
1
0
2019-02-20
1
1
2019-03-06
1
2
2019-03-13
2
0
2020-07-29
2
1
2024-01-17
_citation.journal_volume
_citation.page_first
_citation.page_last
_citation.title
_atom_site.auth_atom_id
_atom_site.label_atom_id
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr2_auth_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
Spain
MICINN
CTQ2013-44367-C2-2-P
Spain
MICINN
BFU2016-75633-P
DGalpNAca
N-acetyl-a-D-galactopyranosamine
a-D-GalpNAc
GalNAc
N
PDBE
Y
PDBE
2018-02-16
REL
REL
EDO
1,2-ETHANEDIOL
A2G
2-acetamido-2-deoxy-alpha-D-galactopyranose
HOH
water
32630
Synthetic construct
sample
1SM3
PDB
experimental model
EDO
1
3
EDO
EDO
1201
H
EDO
2
3
EDO
EDO
1202
H
EDO
3
3
EDO
EDO
1203
H
EDO
4
3
EDO
EDO
1204
H
MOL
901
4
A2G
A2G
101
B
HOH
48
5
HOH
HOH
1301
H
HOH
69
5
HOH
HOH
1302
H
HOH
77
5
HOH
HOH
1303
H
HOH
191
5
HOH
HOH
1304
H
HOH
15
5
HOH
HOH
1305
H
HOH
198
5
HOH
HOH
1306
H
HOH
171
5
HOH
HOH
1307
H
HOH
10
5
HOH
HOH
1308
H
HOH
121
5
HOH
HOH
1309
H
HOH
189
5
HOH
HOH
1310
H
HOH
7
5
HOH
HOH
1311
H
HOH
42
5
HOH
HOH
1312
H
HOH
40
5
HOH
HOH
1313
H
HOH
103
5
HOH
HOH
1314
H
HOH
125
5
HOH
HOH
1315
H
HOH
124
5
HOH
HOH
1316
H
HOH
147
5
HOH
HOH
1317
H
HOH
97
5
HOH
HOH
1318
H
HOH
16
5
HOH
HOH
1319
H
HOH
23
5
HOH
HOH
1320
H
HOH
195
5
HOH
HOH
1321
H
HOH
31
5
HOH
HOH
1322
H
HOH
72
5
HOH
HOH
1323
H
HOH
187
5
HOH
HOH
1324
H
HOH
75
5
HOH
HOH
1325
H
HOH
20
5
HOH
HOH
1326
H
HOH
26
5
HOH
HOH
1327
H
HOH
143
5
HOH
HOH
1328
H
HOH
122
5
HOH
HOH
1329
H
HOH
13
5
HOH
HOH
1330
H
HOH
57
5
HOH
HOH
1331
H
HOH
197
5
HOH
HOH
1332
H
HOH
51
5
HOH
HOH
1333
H
HOH
170
5
HOH
HOH
1334
H
HOH
22
5
HOH
HOH
1335
H
HOH
180
5
HOH
HOH
1336
H
HOH
201
5
HOH
HOH
1337
H
HOH
64
5
HOH
HOH
1338
H
HOH
188
5
HOH
HOH
1339
H
HOH
163
5
HOH
HOH
1340
H
HOH
8
5
HOH
HOH
1341
H
HOH
66
5
HOH
HOH
1342
H
HOH
177
5
HOH
HOH
1343
H
HOH
82
5
HOH
HOH
1344
H
HOH
172
5
HOH
HOH
1345
H
HOH
11
5
HOH
HOH
1346
H
HOH
53
5
HOH
HOH
1347
H
HOH
50
5
HOH
HOH
1348
H
HOH
98
5
HOH
HOH
1349
H
HOH
6
5
HOH
HOH
1350
H
HOH
113
5
HOH
HOH
1351
H
HOH
137
5
HOH
HOH
1352
H
HOH
36
5
HOH
HOH
1353
H
HOH
81
5
HOH
HOH
1354
H
HOH
108
5
HOH
HOH
1355
H
HOH
3
5
HOH
HOH
1356
H
HOH
70
5
HOH
HOH
1357
H
HOH
47
5
HOH
HOH
1358
H
HOH
134
5
HOH
HOH
1359
H
HOH
84
5
HOH
HOH
1360
H
HOH
162
5
HOH
HOH
1361
H
HOH
79
5
HOH
HOH
1362
H
HOH
60
5
HOH
HOH
1363
H
HOH
58
5
HOH
HOH
1364
H
HOH
100
5
HOH
HOH
1365
H
HOH
30
5
HOH
HOH
1366
H
HOH
127
5
HOH
HOH
1367
H
HOH
5
5
HOH
HOH
1368
H
HOH
33
5
HOH
HOH
1369
H
HOH
32
5
HOH
HOH
1370
H
HOH
149
5
HOH
HOH
1371
H
HOH
115
5
HOH
HOH
1372
H
HOH
21
5
HOH
HOH
1373
H
HOH
104
5
HOH
HOH
1374
H
HOH
39
5
HOH
HOH
1375
H
HOH
14
5
HOH
HOH
1376
H
HOH
135
5
HOH
HOH
1377
H
HOH
91
5
HOH
HOH
1378
H
HOH
150
5
HOH
HOH
1379
H
HOH
2
5
HOH
HOH
1380
H
HOH
44
5
HOH
HOH
1381
H
HOH
89
5
HOH
HOH
1382
H
HOH
1
5
HOH
HOH
1383
H
HOH
25
5
HOH
HOH
1384
H
HOH
139
5
HOH
HOH
1385
H
HOH
146
5
HOH
HOH
1386
H
HOH
34
5
HOH
HOH
1387
H
HOH
199
5
HOH
HOH
1388
H
HOH
120
5
HOH
HOH
1389
H
HOH
67
5
HOH
HOH
1390
H
HOH
19
5
HOH
HOH
1391
H
HOH
87
5
HOH
HOH
1392
H
HOH
56
5
HOH
HOH
1393
H
HOH
90
5
HOH
HOH
1394
H
HOH
28
5
HOH
HOH
1395
H
HOH
83
5
HOH
HOH
1396
H
HOH
130
5
HOH
HOH
1397
H
HOH
131
5
HOH
HOH
1398
H
HOH
76
5
HOH
HOH
1399
H
HOH
71
5
HOH
HOH
1400
H
HOH
46
5
HOH
HOH
1401
H
HOH
102
5
HOH
HOH
1402
H
HOH
54
5
HOH
HOH
1403
H
HOH
38
5
HOH
HOH
1404
H
HOH
196
5
HOH
HOH
1405
H
HOH
85
5
HOH
HOH
1406
H
HOH
59
5
HOH
HOH
1407
H
HOH
29
5
HOH
HOH
1408
H
HOH
63
5
HOH
HOH
1409
H
HOH
80
5
HOH
HOH
1410
H
HOH
52
5
HOH
HOH
1411
H
HOH
45
5
HOH
HOH
1412
H
HOH
18
5
HOH
HOH
1413
H
HOH
165
5
HOH
HOH
1414
H
HOH
9
5
HOH
HOH
1415
H
HOH
116
5
HOH
HOH
1416
H
HOH
193
5
HOH
HOH
1417
H
HOH
185
5
HOH
HOH
1418
H
HOH
109
5
HOH
HOH
1419
H
HOH
62
5
HOH
HOH
1420
H
HOH
112
5
HOH
HOH
1421
H
HOH
37
5
HOH
HOH
1422
H
HOH
65
5
HOH
HOH
1423
H
HOH
106
5
HOH
HOH
1424
H
HOH
156
5
HOH
HOH
1425
H
HOH
192
5
HOH
HOH
1426
H
HOH
99
5
HOH
HOH
1427
H
HOH
74
5
HOH
HOH
1428
H
HOH
86
5
HOH
HOH
1429
H
HOH
123
5
HOH
HOH
1430
H
HOH
73
5
HOH
HOH
1431
H
HOH
4
5
HOH
HOH
1432
H
HOH
107
5
HOH
HOH
1433
H
HOH
141
5
HOH
HOH
1434
H
HOH
95
5
HOH
HOH
1435
H
HOH
190
5
HOH
HOH
1436
H
HOH
142
5
HOH
HOH
1437
H
HOH
94
5
HOH
HOH
1438
H
HOH
184
5
HOH
HOH
1439
H
HOH
151
5
HOH
HOH
1440
H
HOH
161
5
HOH
HOH
1441
H
HOH
138
5
HOH
HOH
1442
H
HOH
194
5
HOH
HOH
1443
H
HOH
105
5
HOH
HOH
1444
H
HOH
41
5
HOH
HOH
1445
H
HOH
158
5
HOH
HOH
1446
H
HOH
182
5
HOH
HOH
1447
H
HOH
181
5
HOH
HOH
1448
H
HOH
126
5
HOH
HOH
1449
H
HOH
132
5
HOH
HOH
1450
H
HOH
17
5
HOH
HOH
1451
H
HOH
174
5
HOH
HOH
1452
H
HOH
117
5
HOH
HOH
1453
H
HOH
128
5
HOH
HOH
1454
H
HOH
114
5
HOH
HOH
1455
H
HOH
92
5
HOH
HOH
1456
H
HOH
169
5
HOH
HOH
1457
H
HOH
178
5
HOH
HOH
1458
H
HOH
68
5
HOH
HOH
201
B
HOH
78
5
HOH
HOH
202
B
HOH
186
5
HOH
HOH
203
B
HOH
12
5
HOH
HOH
204
B
HOH
167
5
HOH
HOH
205
B
GLN
1
n
1
GLN
1
H
VAL
2
n
2
VAL
2
H
GLN
3
n
3
GLN
3
H
LEU
4
n
4
LEU
4
H
GLN
5
n
5
GLN
5
H
GLU
6
n
6
GLU
6
H
SER
7
n
7
SER
7
H
GLY
8
n
8
GLY
8
H
GLY
9
n
9
GLY
9
H
GLY
10
n
10
GLY
10
H
LEU
11
n
11
LEU
11
H
VAL
12
n
12
VAL
12
H
GLN
13
n
13
GLN
13
H
PRO
14
n
14
PRO
14
H
GLY
15
n
15
GLY
15
H
GLY
16
n
16
GLY
16
H
SER
17
n
17
SER
17
H
MET
18
n
18
MET
18
H
LYS
19
n
19
LYS
19
H
LEU
20
n
20
LEU
20
H
SER
21
n
21
SER
21
H
CYS
22
n
22
CYS
22
H
VAL
23
n
23
VAL
23
H
ALA
24
n
24
ALA
24
H
SER
25
n
25
SER
25
H
GLY
26
n
26
GLY
26
H
PHE
27
n
27
PHE
27
H
THR
28
n
28
THR
28
H
PHE
29
n
29
PHE
29
H
SER
30
n
30
SER
30
H
ASN
31
n
31
ASN
31
H
TYR
32
n
32
TYR
32
H
TRP
33
n
33
TRP
33
H
MET
34
n
34
MET
34
H
ASN
35
n
35
ASN
35
H
TRP
36
n
36
TRP
36
H
VAL
37
n
37
VAL
37
H
ARG
38
n
38
ARG
38
H
GLN
39
n
39
GLN
39
H
SER
40
n
40
SER
40
H
PRO
41
n
41
PRO
41
H
GLU
42
n
42
GLU
42
H
LYS
43
n
43
LYS
43
H
GLY
44
n
44
GLY
44
H
LEU
45
n
45
LEU
45
H
GLU
46
n
46
GLU
46
H
TRP
47
n
47
TRP
47
H
VAL
48
n
48
VAL
48
H
ALA
49
n
49
ALA
49
H
GLU
50
n
50
GLU
50
H
ILE
51
n
51
ILE
51
H
ARG
52
n
52
ARG
52
H
LEU
53
n
53
LEU
53
H
LYS
54
n
54
LYS
54
H
SER
55
n
55
SER
55
H
ASN
56
n
56
ASN
56
H
ASN
57
n
57
ASN
57
H
TYR
58
n
58
TYR
58
H
ALA
59
n
59
ALA
59
H
THR
60
n
60
THR
60
H
HIS
61
n
61
HIS
61
H
TYR
62
n
62
TYR
62
H
ALA
63
n
63
ALA
63
H
GLU
64
n
64
GLU
64
H
SER
65
n
65
SER
65
H
VAL
66
n
66
VAL
66
H
LYS
67
n
67
LYS
67
H
GLY
68
n
68
GLY
68
H
ARG
69
n
69
ARG
69
H
PHE
70
n
70
PHE
70
H
THR
71
n
71
THR
71
H
ILE
72
n
72
ILE
72
H
SER
73
n
73
SER
73
H
ARG
74
n
74
ARG
74
H
ASP
75
n
75
ASP
75
H
ASP
76
n
76
ASP
76
H
SER
77
n
77
SER
77
H
LYS
78
n
78
LYS
78
H
SER
79
n
79
SER
79
H
SER
80
n
80
SER
80
H
VAL
81
n
81
VAL
81
H
TYR
82
n
82
TYR
82
H
LEU
83
n
83
LEU
83
H
GLN
84
n
84
GLN
84
H
MET
85
n
85
MET
85
H
ASN
86
n
86
ASN
86
H
ASN
87
n
87
ASN
87
H
LEU
88
n
88
LEU
88
H
ARG
89
n
89
ARG
89
H
ALA
90
n
90
ALA
90
H
GLU
91
n
91
GLU
91
H
ASP
92
n
92
ASP
92
H
THR
93
n
93
THR
93
H
GLY
94
n
94
GLY
94
H
ILE
95
n
95
ILE
95
H
TYR
96
n
96
TYR
96
H
TYR
97
n
97
TYR
97
H
CYS
98
n
98
CYS
98
H
THR
99
n
99
THR
99
H
GLY
100
n
100
GLY
100
H
VAL
101
n
101
VAL
101
H
GLY
102
n
102
GLY
102
H
GLN
103
n
103
GLN
103
H
PHE
104
n
104
PHE
104
H
ALA
107
n
105
ALA
107
H
TYR
108
n
106
TYR
108
H
TRP
109
n
107
TRP
109
H
GLY
110
n
108
GLY
110
H
GLN
111
n
109
GLN
111
H
GLY
112
n
110
GLY
112
H
THR
113
n
111
THR
113
H
THR
114
n
112
THR
114
H
VAL
115
n
113
VAL
115
H
THR
116
n
114
THR
116
H
VAL
117
n
115
VAL
117
H
SER
118
n
116
SER
118
H
n
117
990
H
n
118
991
H
n
119
992
H
n
120
993
H
n
121
994
H
n
122
995
H
n
123
996
H
n
124
997
H
n
125
998
H
n
126
999
H
n
127
1000
H
n
128
1001
H
n
129
1002
H
n
130
1003
H
n
131
1004
H
n
132
1005
H
n
133
1006
H
n
134
1007
H
ASP
1008
n
135
ASP
1008
H
ILE
1009
n
136
ILE
1009
H
VAL
1010
n
137
VAL
1010
H
VAL
1011
n
138
VAL
1011
H
THR
1012
n
139
THR
1012
H
GLN
1013
n
140
GLN
1013
H
GLU
1014
n
141
GLU
1014
H
SER
1015
n
142
SER
1015
H
ALA
1016
n
143
ALA
1016
H
LEU
1017
n
144
LEU
1017
H
THR
1018
n
145
THR
1018
H
THR
1019
n
146
THR
1019
H
SER
1020
n
147
SER
1020
H
PRO
1021
n
148
PRO
1021
H
GLY
1022
n
149
GLY
1022
H
GLU
1023
n
150
GLU
1023
H
THR
1024
n
151
THR
1024
H
VAL
1025
n
152
VAL
1025
H
THR
1026
n
153
THR
1026
H
LEU
1027
n
154
LEU
1027
H
THR
1028
n
155
THR
1028
H
CYS
1029
n
156
CYS
1029
H
ARG
1030
n
157
ARG
1030
H
SER
1031
n
158
SER
1031
H
SER
1032
n
159
SER
1032
H
THR
1033
n
160
THR
1033
H
GLY
1034
n
161
GLY
1034
H
ALA
1035
n
162
ALA
1035
H
VAL
1036
n
163
VAL
1036
H
THR
1037
n
164
THR
1037
H
THR
1038
n
165
THR
1038
H
SER
1039
n
166
SER
1039
H
ASN
1040
n
167
ASN
1040
H
TYR
1041
n
168
TYR
1041
H
ALA
1042
n
169
ALA
1042
H
ASN
1043
n
170
ASN
1043
H
TRP
1044
n
171
TRP
1044
H
VAL
1045
n
172
VAL
1045
H
GLN
1046
n
173
GLN
1046
H
GLU
1047
n
174
GLU
1047
H
LYS
1048
n
175
LYS
1048
H
PRO
1049
n
176
PRO
1049
H
ASP
1050
n
177
ASP
1050
H
HIS
1051
n
178
HIS
1051
H
LEU
1052
n
179
LEU
1052
H
PHE
1053
n
180
PHE
1053
H
THR
1054
n
181
THR
1054
H
GLY
1055
n
182
GLY
1055
H
LEU
1056
n
183
LEU
1056
H
ILE
1057
n
184
ILE
1057
H
GLY
1058
n
185
GLY
1058
H
GLY
1059
n
186
GLY
1059
H
THR
1060
n
187
THR
1060
H
ASN
1061
n
188
ASN
1061
H
ASN
1062
n
189
ASN
1062
H
ARG
1063
n
190
ARG
1063
H
ALA
1064
n
191
ALA
1064
H
PRO
1065
n
192
PRO
1065
H
GLY
1066
n
193
GLY
1066
H
VAL
1067
n
194
VAL
1067
H
PRO
1068
n
195
PRO
1068
H
ALA
1069
n
196
ALA
1069
H
ARG
1070
n
197
ARG
1070
H
PHE
1071
n
198
PHE
1071
H
SER
1072
n
199
SER
1072
H
GLY
1073
n
200
GLY
1073
H
SER
1074
n
201
SER
1074
H
LEU
1075
n
202
LEU
1075
H
ILE
1076
n
203
ILE
1076
H
GLY
1077
n
204
GLY
1077
H
ASP
1078
n
205
ASP
1078
H
LYS
1079
n
206
LYS
1079
H
ALA
1080
n
207
ALA
1080
H
ALA
1081
n
208
ALA
1081
H
LEU
1082
n
209
LEU
1082
H
THR
1083
n
210
THR
1083
H
ILE
1084
n
211
ILE
1084
H
THR
1085
n
212
THR
1085
H
GLY
1086
n
213
GLY
1086
H
ALA
1087
n
214
ALA
1087
H
GLN
1088
n
215
GLN
1088
H
THR
1089
n
216
THR
1089
H
GLU
1090
n
217
GLU
1090
H
ASP
1091
n
218
ASP
1091
H
GLU
1092
n
219
GLU
1092
H
ALA
1093
n
220
ALA
1093
H
ILE
1094
n
221
ILE
1094
H
TYR
1095
n
222
TYR
1095
H
PHE
1096
n
223
PHE
1096
H
CYS
1097
n
224
CYS
1097
H
ALA
1098
n
225
ALA
1098
H
LEU
1099
n
226
LEU
1099
H
TRP
1100
n
227
TRP
1100
H
TYR
1101
n
228
TYR
1101
H
SER
1102
n
229
SER
1102
H
ASN
1103
n
230
ASN
1103
H
HIS
1104
n
231
HIS
1104
H
TRP
1105
n
232
TRP
1105
H
VAL
1106
n
233
VAL
1106
H
PHE
1107
n
234
PHE
1107
H
GLY
1108
n
235
GLY
1108
H
GLY
1109
n
236
GLY
1109
H
GLY
1110
n
237
GLY
1110
H
THR
1111
n
238
THR
1111
H
LYS
1112
n
239
LYS
1112
H
LEU
1113
n
240
LEU
1113
H
THR
1114
n
241
THR
1114
H
VAL
1115
n
242
VAL
1115
H
LEU
1116
n
243
LEU
1116
H
GLY
1117
n
244
GLY
1117
H
MOL
901
n
1
ALA
1
B
MOL
901
n
2
PRO
2
B
MOL
901
n
3
ASP
3
B
MOL
901
n
4
T9E
4
B
MOL
901
n
5
ARG
5
B
MOL
901
n
6
PRO
6
B
MOL
901
n
7
NH2
7
B
author_and_software_defined_assembly
PISA
2
dimeric
The molecule is monomeric.
gel filtration
1960
11
10450
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
H
N
SER
7
A
N
SER
7
H
O
SER
21
A
O
SER
21
H
N
MET
18
A
N
MET
18
H
O
MET
85
A
O
MET
85
H
O
TYR
82
A
O
TYR
82
H
N
SER
73
A
N
SER
73
H
N
GLY
10
A
N
GLY
10
H
O
THR
116
A
O
THR
114
H
O
VAL
115
A
O
VAL
113
H
N
GLY
94
A
N
GLY
94
H
O
TYR
97
A
O
TYR
97
H
N
VAL
37
A
N
VAL
37
H
N
ARG
38
A
N
ARG
38
H
O
GLU
46
A
O
GLU
46
H
N
GLU
50
A
N
GLU
50
H
O
HIS
61
A
O
HIS
61
H
N
GLY
10
A
N
GLY
10
H
O
THR
116
A
O
THR
114
H
O
VAL
115
A
O
VAL
113
H
N
GLY
94
A
N
GLY
94
H
N
GLY
100
A
N
GLY
100
H
O
TYR
108
A
O
TYR
106
H
N
THR
1012
A
N
THR
139
H
O
ARG
1030
A
O
ARG
157
H
N
LEU
1027
A
N
LEU
154
H
O
LEU
1082
A
O
LEU
209
H
O
THR
1083
A
O
THR
210
H
N
SER
1072
A
N
SER
199
H
N
THR
1019
A
N
THR
146
H
O
THR
1114
A
O
THR
241
H
O
LEU
1113
A
O
LEU
240
H
N
ALA
1093
A
N
ALA
220
H
O
ILE
1094
A
O
ILE
221
H
N
GLU
1047
A
N
GLU
174
H
N
TRP
1044
A
N
TRP
171
H
O
LEU
1056
A
O
LEU
183
H
N
GLY
1058
A
N
GLY
185
H
O
ASN
1062
A
O
ASN
189
H
N
THR
1019
A
N
THR
146
H
O
THR
1114
A
O
THR
241
H
O
LEU
1113
A
O
LEU
240
H
N
ALA
1093
A
N
ALA
220
H
N
LEU
1099
A
N
LEU
226
H
O
VAL
1106
A
O
VAL
233
1
H
CG
GLN
1
A
CG
GLN
1
1
Y
1
H
CD
GLN
1
A
CD
GLN
1
1
Y
1
H
OE1
GLN
1
A
OE1
GLN
1
1
Y
1
H
NE2
GLN
1
A
NE2
GLN
1
1
Y
1
H
SER
990
A
SER
117
1
Y
1
H
SER
991
A
SER
118
1
Y
1
H
SER
992
A
SER
119
1
Y
1
H
GLY
993
A
GLY
120
1
Y
1
H
GLY
994
A
GLY
121
1
Y
1
H
GLY
995
A
GLY
122
1
Y
1
H
GLY
996
A
GLY
123
1
Y
1
H
SER
997
A
SER
124
1
Y
1
H
GLY
998
A
GLY
125
1
Y
1
H
GLY
999
A
GLY
126
1
Y
1
H
GLY
1000
A
GLY
127
1
Y
1
H
GLY
1001
A
GLY
128
1
Y
1
H
GLY
1002
A
GLY
129
1
Y
1
H
SER
1003
A
SER
130
1
Y
1
H
SER
1004
A
SER
131
1
Y
1
H
GLY
1005
A
GLY
132
1
Y
1
H
SER
1006
A
SER
133
1
Y
1
H
SER
1007
A
SER
134
1
Y
1
3.05
0.50
120.30
123.35
H
H
H
NE
CZ
NH1
ARG
ARG
ARG
69
69
69
N
1
H
H
O1
O1
EDO
EDO
1202
1204
0.00
1_555
4_445
1
H
H
C1
C1
EDO
EDO
1202
1204
0.00
1_555
4_445
1
H
H
C2
C2
EDO
EDO
1202
1204
0.00
1_555
4_445
1
H
H
O2
O2
EDO
EDO
1202
1204
0.00
1_555
4_445
1
H
H
C2
O2
EDO
EDO
1202
1204
1.35
1_555
4_445
1
H
H
O2
C2
EDO
EDO
1202
1204
1.35
1_555
4_445
1
H
H
O1
C1
EDO
EDO
1202
1204
1.38
1_555
4_445
1
H
H
C1
O1
EDO
EDO
1202
1204
1.38
1_555
4_445
1
H
H
C1
C2
EDO
EDO
1202
1204
1.49
1_555
4_445
1
H
H
C2
C1
EDO
EDO
1202
1204
1.49
1_555
4_445
1
H
LYS
43
76.56
-2.32
1
H
ARG
52
-97.33
-158.69
1
H
VAL
101
81.38
105.43
1
H
THR
1060
73.86
-54.68
1
H
ASN
1061
-142.38
18.27
1
H
SER
1102
67.13
-52.73
1
H
ASN
1103
-147.32
18.15
1
B
PRO
2
-77.50
-162.79
24.356
0.25
0.00
0.00
1.65
0.00
-1.90
0.964
0.954
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.22968
0.20480
0.20578
1.40
54.70
1617
39679
3.9
93.28
1.345
0.053
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.074
0.074
0.80
0.80
1.20
1SM3
1.40
54.70
163
1959
16
0
1780
0.007
0.020
1838
0.004
0.020
1628
1.355
1.959
2496
1.105
3.015
3773
6.300
5.000
225
34.245
24.133
75
12.087
15.000
269
18.867
15.000
8
0.075
0.200
279
0.005
0.021
2039
0.001
0.020
389
1.067
2.282
906
1.067
2.281
904
1.856
3.417
1126
1.855
3.417
1126
1.283
2.571
932
1.283
2.571
932
2.121
3.765
1370
4.151
27.619
1980
4.150
27.656
1981
0.352
0.301
1.436
125
3076
20
99.88
1.40
54.70
6FRJ
41360
0.996
0.031
1
12.0
5.3
93.4
1.40
1.48
2.3
0.892
0.327
1
5.4
99.9
refinement
REFMAC
5.8.0189
data reduction
XDS
data scaling
SCALA
phasing
MOLREP
N
Crystal structure of scFv-SM3 in complex with APD-SeThrGalNAc-RP
1
N
N
2
N
N
3
N
N
3
N
N
3
N
N
3
N
N
4
N
N
5
N
N
5
N
N
H
THR
28
A
THR
28
HELX_P
H
TYR
32
A
TYR
32
5
AA1
5
H
LEU
53
A
LEU
53
HELX_P
H
ASN
57
A
ASN
57
5
AA2
5
H
ASP
76
A
ASP
76
HELX_P
H
LYS
78
A
LYS
78
5
AA3
3
H
ARG
89
A
ARG
89
HELX_P
H
THR
93
A
THR
93
5
AA4
5
H
THR
1037
A
THR
164
HELX_P
H
TYR
1041
A
TYR
168
5
AA5
5
H
GLN
1088
A
GLN
215
HELX_P
H
GLU
1092
A
GLU
219
5
AA6
5
disulf
2.038
H
CYS
22
A
SG
CYS
22
1_555
H
CYS
98
A
SG
CYS
98
1_555
disulf
2.064
H
CYS
1029
A
SG
CYS
156
1_555
H
CYS
1097
A
SG
CYS
224
1_555
covale
1.346
both
B
ASP
3
B
C
ASP
3
1_555
B
T9E
4
B
N
T9E
4
1_555
covale
1.356
both
B
T9E
4
B
C
T9E
4
1_555
B
ARG
5
B
N
ARG
5
1_555
covale
1.981
one
B
T9E
4
B
SEG
T9E
4
1_555
B
A2G
101
G
C1
A2G
1_555
covale
1.337
both
B
PRO
6
B
C
PRO
6
1_555
B
NH2
7
B
N
NH2
7
1_555
IMMUNE SYSTEM
IMMUNE SYSTEM, Glycopeptides, antibodies, molecular recognition, conformation analysis
H
GLY
102
A
GLY
102
1
H
GLN
103
A
GLN
103
-13.71
6FRJ
PDB
1
1
6FRJ
6FRJ
PDB
2
1
6FRJ
1
1117
6FRJ
1
1117
6FRJ
H
1
1
244
1
7
6FRJ
1
7
6FRJ
B
2
1
7
4
6
4
4
6
4
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
parallel
anti-parallel
anti-parallel
H
GLN
3
A
GLN
3
H
SER
7
A
SER
7
H
MET
18
A
MET
18
H
SER
25
A
SER
25
H
SER
80
A
SER
80
H
MET
85
A
MET
85
H
PHE
70
A
PHE
70
H
ASP
75
A
ASP
75
H
GLY
10
A
GLY
10
H
VAL
12
A
VAL
12
H
THR
113
A
THR
111
H
VAL
117
A
VAL
115
H
GLY
94
A
GLY
94
H
GLY
100
A
GLY
100
H
MET
34
A
MET
34
H
GLN
39
A
GLN
39
H
LEU
45
A
LEU
45
H
ILE
51
A
ILE
51
H
THR
60
A
THR
60
H
TYR
62
A
TYR
62
H
GLY
10
A
GLY
10
H
VAL
12
A
VAL
12
H
THR
113
A
THR
111
H
VAL
117
A
VAL
115
H
GLY
94
A
GLY
94
H
GLY
100
A
GLY
100
H
TYR
108
A
TYR
106
H
TRP
109
A
TRP
107
H
VAL
1011
A
VAL
138
H
GLN
1013
A
GLN
140
H
THR
1024
A
THR
151
H
SER
1031
A
SER
158
H
LYS
1079
A
LYS
206
H
THR
1085
A
THR
212
H
PHE
1071
A
PHE
198
H
ILE
1076
A
ILE
203
H
ALA
1016
A
ALA
143
H
THR
1019
A
THR
146
H
THR
1111
A
THR
238
H
VAL
1115
A
VAL
242
H
ALA
1093
A
ALA
220
H
TRP
1100
A
TRP
227
H
ASN
1043
A
ASN
170
H
LYS
1048
A
LYS
175
H
LEU
1052
A
LEU
179
H
GLY
1058
A
GLY
185
H
ASN
1062
A
ASN
189
H
ARG
1063
A
ARG
190
H
ALA
1016
A
ALA
143
H
THR
1019
A
THR
146
H
THR
1111
A
THR
238
H
VAL
1115
A
VAL
242
H
ALA
1093
A
ALA
220
H
TRP
1100
A
TRP
227
H
TRP
1105
A
TRP
232
H
PHE
1107
A
PHE
234
19
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