0.007694
0.000000
0.004378
0.000000
0.013604
0.000000
0.000000
0.000000
0.014122
0.00000
0.00000
0.00000
Terai, T.
Maki, E.
Sugiyama, S.
Takahashi, Y.
Matsumura, H.
Mori, Y.
Nagano, T.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
16
90.00
119.64
90.00
129.967
73.510
81.473
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
C8 H15 N O6
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE
D-saccharide, beta 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
O4 S -2
96.063
SULFATE ION
non-polymer
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
C12 H20 N2 O3 S
272.364
5-[(3aS,4S,6aR)-1,3-dimethyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
non-polymer
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
R
C
N
251
R
C
N
252
R
C
N
253
S
C
N
254
R
C
N
255
N
C
N
256
N
C
N
257
N
C
N
258
N
N
N
259
N
O
N
260
N
O
N
261
N
O
N
262
N
O
N
263
N
O
N
264
N
O
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
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
N
N
281
S
C
N
282
N
C
N
283
N
O
N
284
N
C
Y
285
N
C
Y
286
N
C
Y
287
N
C
Y
288
N
C
Y
289
N
C
Y
290
N
C
N
291
N
O
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
H
N
302
N
H
N
303
N
N
N
304
S
C
N
305
N
C
N
306
N
O
N
307
N
C
N
308
N
C
N
309
N
C
N
310
N
O
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
N
N
321
S
C
N
322
N
C
N
323
N
O
N
324
N
C
N
325
N
O
N
326
N
O
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
H
N
334
N
S
N
335
N
O
N
336
N
O
N
337
N
O
N
338
N
O
N
339
N
N
N
340
S
C
N
341
N
C
N
342
N
O
N
343
R
C
N
344
N
O
N
345
N
C
N
346
N
O
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
N
N
357
S
C
N
358
N
C
N
359
N
O
N
360
N
C
Y
361
N
C
Y
362
N
C
Y
363
N
C
Y
364
N
N
Y
365
N
C
Y
366
N
C
Y
367
N
C
Y
368
N
C
Y
369
N
C
N
370
N
O
N
371
N
H
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
H
N
382
N
H
N
383
N
N
N
384
S
C
N
385
N
C
N
386
N
O
N
387
N
C
Y
388
N
C
Y
389
N
C
Y
390
N
C
Y
391
N
C
Y
392
N
C
Y
393
N
C
N
394
N
O
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
N
N
408
S
C
N
409
N
C
N
410
N
O
N
411
N
C
N
412
N
C
N
413
N
C
N
414
N
O
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
N
N
427
N
S
N
428
S
C
N
429
N
N
N
430
N
C
N
431
N
O
N
432
S
C
N
433
R
C
N
434
N
C
N
435
N
C
N
436
N
C
N
437
N
C
N
438
N
C
N
439
N
C
N
440
N
O
N
441
N
O
N
442
N
C
N
443
N
C
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
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
462
N
H
N
463
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
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
doub
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
doub
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
Y
278
N
doub
Y
279
N
sing
Y
280
N
sing
N
281
N
sing
Y
282
N
doub
N
283
N
sing
Y
284
N
doub
N
285
N
sing
Y
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
sing
N
313
N
doub
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
doub
N
321
N
doub
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
doub
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
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
doub
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
Y
351
N
doub
Y
352
N
sing
Y
353
N
sing
N
354
N
sing
Y
355
N
doub
Y
356
N
sing
Y
357
N
sing
N
358
N
sing
Y
359
N
sing
Y
360
N
doub
N
361
N
sing
Y
362
N
doub
N
363
N
sing
Y
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
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
doub
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
Y
379
N
doub
Y
380
N
sing
Y
381
N
sing
N
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
sing
N
398
N
doub
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
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
sing
N
415
N
sing
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
N
420
N
doub
N
421
N
sing
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
doub
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
sing
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
UK
Chem.Biol.
CBOLE2
2050
1074-5521
18
1261
1272
10.1016/j.chembiol.2011.09.007
22035795
Rational development of caged-biotin protein-labeling agents and some applications in live cells
2011
10.2210/pdb3vhh/pdb
pdb_00003vhh
100
1
CCD
2010-11-18
RAYONIX MX225HE
SINGLE WAVELENGTH
M
x-ray
1
0.9
1.0
BL44XU
SPring-8
0.9
SYNCHROTRON
SPRING-8 BEAMLINE BL44XU
13716.431
Avidin
UNP residues 25-147
4
nat
polymer
272.364
5-[(3aS,4S,6aR)-1,3-dimethyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
4
syn
non-polymer
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
4
man
non-polymer
96.063
SULFATE ION
6
syn
non-polymer
18.015
water
123
nat
water
no
no
ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFT
GQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL
ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFT
GQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL
A,B,C,D
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
chicken
sample
9031
Gallus gallus
1
3.08
60.10
VAPOR DIFFUSION, SITTING DROP
5
2.5-2.7M ammonium sulfate, 0.1M sodium citrate(pH 4.0-5.0), vapor diffusion, sitting drop, temperature 293K
293
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
repository
Initial release
Carbohydrate remediation
repository
Remediation
Data collection
Derived calculations
Structure summary
Data collection
Database references
Refinement description
Structure summary
1
0
2011-12-28
1
1
2020-07-29
1
2
2023-11-08
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_pdbx_entity_nonpoly.name
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_role
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
PDBJ
Y
PDBJ
2011-08-25
REL
REL
VHH
5-[(3aS,4S,6aR)-1,3-dimethyl-2-oxohexahydro-1H-thieno[3,4-d]imidazol-4-yl]pentanoic acid
NAG
2-acetamido-2-deoxy-beta-D-glucopyranose
SO4
SULFATE ION
HOH
water
1AVD
PDB
experimental model
DME
1124
2
VHH
VHH
1124
A
NAG
1125
3
NAG
NAG
1125
A
SO4
1126
4
SO4
SO4
1126
A
SO4
1127
4
SO4
SO4
1127
A
DME
1124
2
VHH
VHH
1124
B
NAG
1125
3
NAG
NAG
1125
B
SO4
1126
4
SO4
SO4
1126
B
DME
1124
2
VHH
VHH
1124
C
NAG
1125
3
NAG
NAG
1125
C
SO4
1126
4
SO4
SO4
1126
C
SO4
1127
4
SO4
SO4
1127
C
DME
1124
2
VHH
VHH
1124
D
NAG
1125
3
NAG
NAG
1125
D
SO4
1126
4
SO4
SO4
1126
D
HOH
124
5
HOH
HOH
124
A
HOH
125
5
HOH
HOH
125
A
HOH
3
5
HOH
HOH
126
A
HOH
13
5
HOH
HOH
127
A
HOH
14
5
HOH
HOH
128
A
HOH
15
5
HOH
HOH
129
A
HOH
16
5
HOH
HOH
130
A
HOH
17
5
HOH
HOH
131
A
HOH
132
5
HOH
HOH
132
A
HOH
21
5
HOH
HOH
133
A
HOH
22
5
HOH
HOH
134
A
HOH
23
5
HOH
HOH
135
A
HOH
24
5
HOH
HOH
136
A
HOH
25
5
HOH
HOH
137
A
HOH
32
5
HOH
HOH
138
A
HOH
33
5
HOH
HOH
139
A
HOH
34
5
HOH
HOH
140
A
HOH
35
5
HOH
HOH
141
A
HOH
36
5
HOH
HOH
142
A
HOH
37
5
HOH
HOH
143
A
HOH
42
5
HOH
HOH
144
A
HOH
43
5
HOH
HOH
145
A
HOH
46
5
HOH
HOH
146
A
HOH
47
5
HOH
HOH
147
A
HOH
48
5
HOH
HOH
148
A
HOH
51
5
HOH
HOH
149
A
HOH
57
5
HOH
HOH
150
A
HOH
58
5
HOH
HOH
151
A
HOH
59
5
HOH
HOH
152
A
HOH
61
5
HOH
HOH
153
A
HOH
123
5
HOH
HOH
154
A
HOH
19
5
HOH
HOH
124
B
HOH
27
5
HOH
HOH
125
B
HOH
126
5
HOH
HOH
126
B
HOH
28
5
HOH
HOH
127
B
HOH
29
5
HOH
HOH
128
B
HOH
30
5
HOH
HOH
129
B
HOH
44
5
HOH
HOH
130
B
HOH
45
5
HOH
HOH
131
B
HOH
49
5
HOH
HOH
132
B
HOH
50
5
HOH
HOH
133
B
HOH
52
5
HOH
HOH
134
B
HOH
53
5
HOH
HOH
135
B
HOH
54
5
HOH
HOH
136
B
HOH
55
5
HOH
HOH
137
B
HOH
56
5
HOH
HOH
138
B
HOH
63
5
HOH
HOH
139
B
HOH
65
5
HOH
HOH
140
B
HOH
66
5
HOH
HOH
141
B
HOH
67
5
HOH
HOH
142
B
HOH
69
5
HOH
HOH
143
B
HOH
70
5
HOH
HOH
144
B
HOH
71
5
HOH
HOH
145
B
HOH
72
5
HOH
HOH
146
B
HOH
73
5
HOH
HOH
147
B
HOH
74
5
HOH
HOH
148
B
HOH
77
5
HOH
HOH
149
B
HOH
78
5
HOH
HOH
150
B
HOH
83
5
HOH
HOH
151
B
HOH
1
5
HOH
HOH
124
C
HOH
2
5
HOH
HOH
125
C
HOH
4
5
HOH
HOH
126
C
HOH
127
5
HOH
HOH
127
C
HOH
128
5
HOH
HOH
128
C
HOH
129
5
HOH
HOH
129
C
HOH
5
5
HOH
HOH
130
C
HOH
6
5
HOH
HOH
131
C
HOH
7
5
HOH
HOH
132
C
HOH
133
5
HOH
HOH
133
C
HOH
10
5
HOH
HOH
134
C
HOH
11
5
HOH
HOH
135
C
HOH
12
5
HOH
HOH
136
C
HOH
41
5
HOH
HOH
137
C
HOH
75
5
HOH
HOH
138
C
HOH
82
5
HOH
HOH
139
C
HOH
86
5
HOH
HOH
140
C
HOH
87
5
HOH
HOH
141
C
HOH
95
5
HOH
HOH
142
C
HOH
98
5
HOH
HOH
143
C
HOH
100
5
HOH
HOH
144
C
HOH
101
5
HOH
HOH
145
C
HOH
104
5
HOH
HOH
146
C
HOH
105
5
HOH
HOH
147
C
HOH
106
5
HOH
HOH
148
C
HOH
107
5
HOH
HOH
149
C
HOH
108
5
HOH
HOH
150
C
HOH
109
5
HOH
HOH
151
C
HOH
112
5
HOH
HOH
152
C
HOH
113
5
HOH
HOH
153
C
HOH
114
5
HOH
HOH
154
C
HOH
115
5
HOH
HOH
155
C
HOH
117
5
HOH
HOH
156
C
HOH
9
5
HOH
HOH
124
D
HOH
18
5
HOH
HOH
125
D
HOH
20
5
HOH
HOH
126
D
HOH
26
5
HOH
HOH
127
D
HOH
38
5
HOH
HOH
128
D
HOH
39
5
HOH
HOH
129
D
HOH
130
5
HOH
HOH
130
D
HOH
131
5
HOH
HOH
131
D
HOH
40
5
HOH
HOH
132
D
HOH
76
5
HOH
HOH
133
D
HOH
79
5
HOH
HOH
134
D
HOH
80
5
HOH
HOH
135
D
HOH
81
5
HOH
HOH
136
D
HOH
88
5
HOH
HOH
137
D
HOH
89
5
HOH
HOH
138
D
HOH
90
5
HOH
HOH
139
D
HOH
91
5
HOH
HOH
140
D
HOH
92
5
HOH
HOH
141
D
HOH
94
5
HOH
HOH
142
D
HOH
96
5
HOH
HOH
143
D
HOH
97
5
HOH
HOH
144
D
HOH
99
5
HOH
HOH
145
D
HOH
102
5
HOH
HOH
146
D
HOH
103
5
HOH
HOH
147
D
HOH
110
5
HOH
HOH
148
D
HOH
111
5
HOH
HOH
149
D
HOH
118
5
HOH
HOH
150
D
HOH
119
5
HOH
HOH
151
D
HOH
120
5
HOH
HOH
152
D
HOH
121
5
HOH
HOH
153
D
HOH
122
5
HOH
HOH
154
D
ALA
1
n
1
ALA
1
A
ARG
2
n
2
ARG
2
A
LYS
3
n
3
LYS
3
A
CYS
4
n
4
CYS
4
A
SER
5
n
5
SER
5
A
LEU
6
n
6
LEU
6
A
THR
7
n
7
THR
7
A
GLY
8
n
8
GLY
8
A
LYS
9
n
9
LYS
9
A
TRP
10
n
10
TRP
10
A
THR
11
n
11
THR
11
A
ASN
12
n
12
ASN
12
A
ASP
13
n
13
ASP
13
A
LEU
14
n
14
LEU
14
A
GLY
15
n
15
GLY
15
A
SER
16
n
16
SER
16
A
ASN
17
n
17
ASN
17
A
MET
18
n
18
MET
18
A
THR
19
n
19
THR
19
A
ILE
20
n
20
ILE
20
A
GLY
21
n
21
GLY
21
A
ALA
22
n
22
ALA
22
A
VAL
23
n
23
VAL
23
A
ASN
24
n
24
ASN
24
A
SER
25
n
25
SER
25
A
ARG
26
n
26
ARG
26
A
GLY
27
n
27
GLY
27
A
GLU
28
n
28
GLU
28
A
PHE
29
n
29
PHE
29
A
THR
30
n
30
THR
30
A
GLY
31
n
31
GLY
31
A
THR
32
n
32
THR
32
A
TYR
33
n
33
TYR
33
A
ILE
34
n
34
ILE
34
A
THR
35
n
35
THR
35
A
ALA
36
n
36
ALA
36
A
VAL
37
n
37
VAL
37
A
THR
38
n
38
THR
38
A
ALA
39
n
39
ALA
39
A
THR
40
n
40
THR
40
A
SER
41
n
41
SER
41
A
ASN
42
n
42
ASN
42
A
GLU
43
n
43
GLU
43
A
ILE
44
n
44
ILE
44
A
LYS
45
n
45
LYS
45
A
GLU
46
n
46
GLU
46
A
SER
47
n
47
SER
47
A
PRO
48
n
48
PRO
48
A
LEU
49
n
49
LEU
49
A
HIS
50
n
50
HIS
50
A
GLY
51
n
51
GLY
51
A
THR
52
n
52
THR
52
A
GLN
53
n
53
GLN
53
A
ASN
54
n
54
ASN
54
A
THR
55
n
55
THR
55
A
ILE
56
n
56
ILE
56
A
ASN
57
n
57
ASN
57
A
LYS
58
n
58
LYS
58
A
ARG
59
n
59
ARG
59
A
THR
60
n
60
THR
60
A
GLN
61
n
61
GLN
61
A
PRO
62
n
62
PRO
62
A
THR
63
n
63
THR
63
A
PHE
64
n
64
PHE
64
A
GLY
65
n
65
GLY
65
A
PHE
66
n
66
PHE
66
A
THR
67
n
67
THR
67
A
VAL
68
n
68
VAL
68
A
ASN
69
n
69
ASN
69
A
TRP
70
n
70
TRP
70
A
LYS
71
n
71
LYS
71
A
PHE
72
n
72
PHE
72
A
SER
73
n
73
SER
73
A
GLU
74
n
74
GLU
74
A
SER
75
n
75
SER
75
A
THR
76
n
76
THR
76
A
THR
77
n
77
THR
77
A
VAL
78
n
78
VAL
78
A
PHE
79
n
79
PHE
79
A
THR
80
n
80
THR
80
A
GLY
81
n
81
GLY
81
A
GLN
82
n
82
GLN
82
A
CYS
83
n
83
CYS
83
A
PHE
84
n
84
PHE
84
A
ILE
85
n
85
ILE
85
A
ASP
86
n
86
ASP
86
A
ARG
87
n
87
ARG
87
A
ASN
88
n
88
ASN
88
A
GLY
89
n
89
GLY
89
A
LYS
90
n
90
LYS
90
A
GLU
91
n
91
GLU
91
A
VAL
92
n
92
VAL
92
A
LEU
93
n
93
LEU
93
A
LYS
94
n
94
LYS
94
A
THR
95
n
95
THR
95
A
MET
96
n
96
MET
96
A
TRP
97
n
97
TRP
97
A
LEU
98
n
98
LEU
98
A
LEU
99
n
99
LEU
99
A
ARG
100
n
100
ARG
100
A
SER
101
n
101
SER
101
A
SER
102
n
102
SER
102
A
VAL
103
n
103
VAL
103
A
ASN
104
n
104
ASN
104
A
ASP
105
n
105
ASP
105
A
ILE
106
n
106
ILE
106
A
GLY
107
n
107
GLY
107
A
ASP
108
n
108
ASP
108
A
ASP
109
n
109
ASP
109
A
TRP
110
n
110
TRP
110
A
LYS
111
n
111
LYS
111
A
ALA
112
n
112
ALA
112
A
THR
113
n
113
THR
113
A
ARG
114
n
114
ARG
114
A
VAL
115
n
115
VAL
115
A
GLY
116
n
116
GLY
116
A
ILE
117
n
117
ILE
117
A
ASN
118
n
118
ASN
118
A
ILE
119
n
119
ILE
119
A
PHE
120
n
120
PHE
120
A
THR
121
n
121
THR
121
A
ARG
122
n
122
ARG
122
A
LEU
123
n
123
LEU
123
A
n
1
1
B
n
2
2
B
LYS
3
n
3
LYS
3
B
CYS
4
n
4
CYS
4
B
SER
5
n
5
SER
5
B
LEU
6
n
6
LEU
6
B
THR
7
n
7
THR
7
B
GLY
8
n
8
GLY
8
B
LYS
9
n
9
LYS
9
B
TRP
10
n
10
TRP
10
B
THR
11
n
11
THR
11
B
ASN
12
n
12
ASN
12
B
ASP
13
n
13
ASP
13
B
LEU
14
n
14
LEU
14
B
GLY
15
n
15
GLY
15
B
SER
16
n
16
SER
16
B
ASN
17
n
17
ASN
17
B
MET
18
n
18
MET
18
B
THR
19
n
19
THR
19
B
ILE
20
n
20
ILE
20
B
GLY
21
n
21
GLY
21
B
ALA
22
n
22
ALA
22
B
VAL
23
n
23
VAL
23
B
ASN
24
n
24
ASN
24
B
SER
25
n
25
SER
25
B
ARG
26
n
26
ARG
26
B
GLY
27
n
27
GLY
27
B
GLU
28
n
28
GLU
28
B
PHE
29
n
29
PHE
29
B
THR
30
n
30
THR
30
B
GLY
31
n
31
GLY
31
B
THR
32
n
32
THR
32
B
TYR
33
n
33
TYR
33
B
ILE
34
n
34
ILE
34
B
THR
35
n
35
THR
35
B
ALA
36
n
36
ALA
36
B
VAL
37
n
37
VAL
37
B
THR
38
n
38
THR
38
B
ALA
39
n
39
ALA
39
B
THR
40
n
40
THR
40
B
SER
41
n
41
SER
41
B
ASN
42
n
42
ASN
42
B
GLU
43
n
43
GLU
43
B
ILE
44
n
44
ILE
44
B
LYS
45
n
45
LYS
45
B
GLU
46
n
46
GLU
46
B
SER
47
n
47
SER
47
B
PRO
48
n
48
PRO
48
B
LEU
49
n
49
LEU
49
B
HIS
50
n
50
HIS
50
B
GLY
51
n
51
GLY
51
B
THR
52
n
52
THR
52
B
GLN
53
n
53
GLN
53
B
ASN
54
n
54
ASN
54
B
THR
55
n
55
THR
55
B
ILE
56
n
56
ILE
56
B
ASN
57
n
57
ASN
57
B
LYS
58
n
58
LYS
58
B
ARG
59
n
59
ARG
59
B
THR
60
n
60
THR
60
B
GLN
61
n
61
GLN
61
B
PRO
62
n
62
PRO
62
B
THR
63
n
63
THR
63
B
PHE
64
n
64
PHE
64
B
GLY
65
n
65
GLY
65
B
PHE
66
n
66
PHE
66
B
THR
67
n
67
THR
67
B
VAL
68
n
68
VAL
68
B
ASN
69
n
69
ASN
69
B
TRP
70
n
70
TRP
70
B
LYS
71
n
71
LYS
71
B
PHE
72
n
72
PHE
72
B
SER
73
n
73
SER
73
B
GLU
74
n
74
GLU
74
B
SER
75
n
75
SER
75
B
THR
76
n
76
THR
76
B
THR
77
n
77
THR
77
B
VAL
78
n
78
VAL
78
B
PHE
79
n
79
PHE
79
B
THR
80
n
80
THR
80
B
GLY
81
n
81
GLY
81
B
GLN
82
n
82
GLN
82
B
CYS
83
n
83
CYS
83
B
PHE
84
n
84
PHE
84
B
ILE
85
n
85
ILE
85
B
ASP
86
n
86
ASP
86
B
ARG
87
n
87
ARG
87
B
ASN
88
n
88
ASN
88
B
GLY
89
n
89
GLY
89
B
LYS
90
n
90
LYS
90
B
GLU
91
n
91
GLU
91
B
VAL
92
n
92
VAL
92
B
LEU
93
n
93
LEU
93
B
LYS
94
n
94
LYS
94
B
THR
95
n
95
THR
95
B
MET
96
n
96
MET
96
B
TRP
97
n
97
TRP
97
B
LEU
98
n
98
LEU
98
B
LEU
99
n
99
LEU
99
B
ARG
100
n
100
ARG
100
B
SER
101
n
101
SER
101
B
SER
102
n
102
SER
102
B
VAL
103
n
103
VAL
103
B
ASN
104
n
104
ASN
104
B
ASP
105
n
105
ASP
105
B
ILE
106
n
106
ILE
106
B
GLY
107
n
107
GLY
107
B
ASP
108
n
108
ASP
108
B
ASP
109
n
109
ASP
109
B
TRP
110
n
110
TRP
110
B
LYS
111
n
111
LYS
111
B
ALA
112
n
112
ALA
112
B
THR
113
n
113
THR
113
B
ARG
114
n
114
ARG
114
B
VAL
115
n
115
VAL
115
B
GLY
116
n
116
GLY
116
B
ILE
117
n
117
ILE
117
B
ASN
118
n
118
ASN
118
B
ILE
119
n
119
ILE
119
B
PHE
120
n
120
PHE
120
B
THR
121
n
121
THR
121
B
ARG
122
n
122
ARG
122
B
LEU
123
n
123
LEU
123
B
ALA
1
n
1
ALA
1
C
ARG
2
n
2
ARG
2
C
LYS
3
n
3
LYS
3
C
CYS
4
n
4
CYS
4
C
SER
5
n
5
SER
5
C
LEU
6
n
6
LEU
6
C
THR
7
n
7
THR
7
C
GLY
8
n
8
GLY
8
C
LYS
9
n
9
LYS
9
C
TRP
10
n
10
TRP
10
C
THR
11
n
11
THR
11
C
ASN
12
n
12
ASN
12
C
ASP
13
n
13
ASP
13
C
LEU
14
n
14
LEU
14
C
GLY
15
n
15
GLY
15
C
SER
16
n
16
SER
16
C
ASN
17
n
17
ASN
17
C
MET
18
n
18
MET
18
C
THR
19
n
19
THR
19
C
ILE
20
n
20
ILE
20
C
GLY
21
n
21
GLY
21
C
ALA
22
n
22
ALA
22
C
VAL
23
n
23
VAL
23
C
ASN
24
n
24
ASN
24
C
SER
25
n
25
SER
25
C
ARG
26
n
26
ARG
26
C
GLY
27
n
27
GLY
27
C
GLU
28
n
28
GLU
28
C
PHE
29
n
29
PHE
29
C
THR
30
n
30
THR
30
C
GLY
31
n
31
GLY
31
C
THR
32
n
32
THR
32
C
TYR
33
n
33
TYR
33
C
ILE
34
n
34
ILE
34
C
THR
35
n
35
THR
35
C
ALA
36
n
36
ALA
36
C
VAL
37
n
37
VAL
37
C
THR
38
n
38
THR
38
C
ALA
39
n
39
ALA
39
C
THR
40
n
40
THR
40
C
SER
41
n
41
SER
41
C
ALA
42
n
42
ASN
42
C
GLU
43
n
43
GLU
43
C
ILE
44
n
44
ILE
44
C
LYS
45
n
45
LYS
45
C
GLU
46
n
46
GLU
46
C
SER
47
n
47
SER
47
C
PRO
48
n
48
PRO
48
C
LEU
49
n
49
LEU
49
C
HIS
50
n
50
HIS
50
C
GLY
51
n
51
GLY
51
C
THR
52
n
52
THR
52
C
GLN
53
n
53
GLN
53
C
ASN
54
n
54
ASN
54
C
THR
55
n
55
THR
55
C
ILE
56
n
56
ILE
56
C
ASN
57
n
57
ASN
57
C
LYS
58
n
58
LYS
58
C
ARG
59
n
59
ARG
59
C
THR
60
n
60
THR
60
C
GLN
61
n
61
GLN
61
C
PRO
62
n
62
PRO
62
C
THR
63
n
63
THR
63
C
PHE
64
n
64
PHE
64
C
GLY
65
n
65
GLY
65
C
PHE
66
n
66
PHE
66
C
THR
67
n
67
THR
67
C
VAL
68
n
68
VAL
68
C
ASN
69
n
69
ASN
69
C
TRP
70
n
70
TRP
70
C
LYS
71
n
71
LYS
71
C
PHE
72
n
72
PHE
72
C
SER
73
n
73
SER
73
C
GLU
74
n
74
GLU
74
C
SER
75
n
75
SER
75
C
THR
76
n
76
THR
76
C
THR
77
n
77
THR
77
C
VAL
78
n
78
VAL
78
C
PHE
79
n
79
PHE
79
C
THR
80
n
80
THR
80
C
GLY
81
n
81
GLY
81
C
GLN
82
n
82
GLN
82
C
CYS
83
n
83
CYS
83
C
PHE
84
n
84
PHE
84
C
ILE
85
n
85
ILE
85
C
ASP
86
n
86
ASP
86
C
ARG
87
n
87
ARG
87
C
ASN
88
n
88
ASN
88
C
GLY
89
n
89
GLY
89
C
LYS
90
n
90
LYS
90
C
GLU
91
n
91
GLU
91
C
VAL
92
n
92
VAL
92
C
LEU
93
n
93
LEU
93
C
LYS
94
n
94
LYS
94
C
THR
95
n
95
THR
95
C
MET
96
n
96
MET
96
C
TRP
97
n
97
TRP
97
C
LEU
98
n
98
LEU
98
C
LEU
99
n
99
LEU
99
C
ARG
100
n
100
ARG
100
C
SER
101
n
101
SER
101
C
SER
102
n
102
SER
102
C
VAL
103
n
103
VAL
103
C
ASN
104
n
104
ASN
104
C
ASP
105
n
105
ASP
105
C
ILE
106
n
106
ILE
106
C
GLY
107
n
107
GLY
107
C
ASP
108
n
108
ASP
108
C
ASP
109
n
109
ASP
109
C
TRP
110
n
110
TRP
110
C
LYS
111
n
111
LYS
111
C
ALA
112
n
112
ALA
112
C
THR
113
n
113
THR
113
C
ARG
114
n
114
ARG
114
C
VAL
115
n
115
VAL
115
C
GLY
116
n
116
GLY
116
C
ILE
117
n
117
ILE
117
C
ASN
118
n
118
ASN
118
C
ILE
119
n
119
ILE
119
C
PHE
120
n
120
PHE
120
C
THR
121
n
121
THR
121
C
ARG
122
n
122
ARG
122
C
LEU
123
n
123
LEU
123
C
n
1
1
D
n
2
2
D
LYS
3
n
3
LYS
3
D
CYS
4
n
4
CYS
4
D
SER
5
n
5
SER
5
D
LEU
6
n
6
LEU
6
D
THR
7
n
7
THR
7
D
GLY
8
n
8
GLY
8
D
LYS
9
n
9
LYS
9
D
TRP
10
n
10
TRP
10
D
THR
11
n
11
THR
11
D
ASN
12
n
12
ASN
12
D
ASP
13
n
13
ASP
13
D
LEU
14
n
14
LEU
14
D
GLY
15
n
15
GLY
15
D
SER
16
n
16
SER
16
D
ASN
17
n
17
ASN
17
D
MET
18
n
18
MET
18
D
THR
19
n
19
THR
19
D
ILE
20
n
20
ILE
20
D
GLY
21
n
21
GLY
21
D
ALA
22
n
22
ALA
22
D
VAL
23
n
23
VAL
23
D
ASN
24
n
24
ASN
24
D
SER
25
n
25
SER
25
D
ARG
26
n
26
ARG
26
D
GLY
27
n
27
GLY
27
D
GLU
28
n
28
GLU
28
D
PHE
29
n
29
PHE
29
D
THR
30
n
30
THR
30
D
GLY
31
n
31
GLY
31
D
THR
32
n
32
THR
32
D
TYR
33
n
33
TYR
33
D
ILE
34
n
34
ILE
34
D
THR
35
n
35
THR
35
D
ALA
36
n
36
ALA
36
D
VAL
37
n
37
VAL
37
D
THR
38
n
38
THR
38
D
ALA
39
n
39
ALA
39
D
THR
40
n
40
THR
40
D
SER
41
n
41
SER
41
D
ASN
42
n
42
ASN
42
D
GLU
43
n
43
GLU
43
D
ILE
44
n
44
ILE
44
D
LYS
45
n
45
LYS
45
D
GLU
46
n
46
GLU
46
D
SER
47
n
47
SER
47
D
PRO
48
n
48
PRO
48
D
LEU
49
n
49
LEU
49
D
HIS
50
n
50
HIS
50
D
GLY
51
n
51
GLY
51
D
THR
52
n
52
THR
52
D
GLN
53
n
53
GLN
53
D
ASN
54
n
54
ASN
54
D
THR
55
n
55
THR
55
D
ILE
56
n
56
ILE
56
D
ASN
57
n
57
ASN
57
D
LYS
58
n
58
LYS
58
D
ARG
59
n
59
ARG
59
D
THR
60
n
60
THR
60
D
GLN
61
n
61
GLN
61
D
PRO
62
n
62
PRO
62
D
THR
63
n
63
THR
63
D
PHE
64
n
64
PHE
64
D
GLY
65
n
65
GLY
65
D
PHE
66
n
66
PHE
66
D
THR
67
n
67
THR
67
D
VAL
68
n
68
VAL
68
D
ASN
69
n
69
ASN
69
D
TRP
70
n
70
TRP
70
D
LYS
71
n
71
LYS
71
D
PHE
72
n
72
PHE
72
D
SER
73
n
73
SER
73
D
GLU
74
n
74
GLU
74
D
SER
75
n
75
SER
75
D
THR
76
n
76
THR
76
D
THR
77
n
77
THR
77
D
VAL
78
n
78
VAL
78
D
PHE
79
n
79
PHE
79
D
THR
80
n
80
THR
80
D
GLY
81
n
81
GLY
81
D
GLN
82
n
82
GLN
82
D
CYS
83
n
83
CYS
83
D
PHE
84
n
84
PHE
84
D
ILE
85
n
85
ILE
85
D
ASP
86
n
86
ASP
86
D
ARG
87
n
87
ARG
87
D
ASN
88
n
88
ASN
88
D
GLY
89
n
89
GLY
89
D
LYS
90
n
90
LYS
90
D
GLU
91
n
91
GLU
91
D
VAL
92
n
92
VAL
92
D
LEU
93
n
93
LEU
93
D
LYS
94
n
94
LYS
94
D
THR
95
n
95
THR
95
D
MET
96
n
96
MET
96
D
TRP
97
n
97
TRP
97
D
LEU
98
n
98
LEU
98
D
LEU
99
n
99
LEU
99
D
ARG
100
n
100
ARG
100
D
SER
101
n
101
SER
101
D
SER
102
n
102
SER
102
D
VAL
103
n
103
VAL
103
D
ASN
104
n
104
ASN
104
D
ASP
105
n
105
ASP
105
D
ILE
106
n
106
ILE
106
D
GLY
107
n
107
GLY
107
D
ASP
108
n
108
ASP
108
D
ASP
109
n
109
ASP
109
D
TRP
110
n
110
TRP
110
D
LYS
111
n
111
LYS
111
D
ALA
112
n
112
ALA
112
D
THR
113
n
113
THR
113
D
ARG
114
n
114
ARG
114
D
VAL
115
n
115
VAL
115
D
GLY
116
n
116
GLY
116
D
ILE
117
n
117
ILE
117
D
ASN
118
n
118
ASN
118
D
ILE
119
n
119
ILE
119
D
PHE
120
n
120
PHE
120
D
THR
121
n
121
THR
121
D
ARG
122
n
122
ARG
122
D
LEU
123
n
123
LEU
123
D
author_and_software_defined_assembly
PISA
4
tetrameric
12640
-104
19850
A
ASN
17
GLYCOSYLATION SITE
A
ASN
17
ASN
B
ASN
17
GLYCOSYLATION SITE
B
ASN
17
ASN
C
ASN
17
GLYCOSYLATION SITE
C
ASN
17
ASN
D
ASN
17
GLYCOSYLATION SITE
D
ASN
17
ASN
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
TRP
10
A
N
TRP
10
A
O
MET
18
A
O
MET
18
A
N
ASN
17
A
N
ASN
17
A
O
ILE
34
A
O
ILE
34
A
N
TYR
33
A
N
TYR
33
A
O
SER
47
A
O
SER
47
A
N
THR
52
A
N
THR
52
A
O
GLY
65
A
O
GLY
65
A
N
VAL
68
A
N
VAL
68
A
O
THR
77
A
O
THR
77
A
N
THR
76
A
N
THR
76
A
O
ARG
100
A
O
ARG
100
A
N
LEU
99
A
N
LEU
99
A
O
ARG
114
A
O
ARG
114
A
O
THR
121
A
O
THR
121
A
N
THR
11
A
N
THR
11
B
N
GLY
8
B
N
GLY
8
B
O
ILE
20
B
O
ILE
20
B
N
ASN
17
B
N
ASN
17
B
O
ILE
34
B
O
ILE
34
B
N
TYR
33
B
N
TYR
33
B
O
SER
47
B
O
SER
47
B
N
HIS
50
B
N
HIS
50
B
O
THR
67
B
O
THR
67
B
N
VAL
68
B
N
VAL
68
B
O
THR
77
B
O
THR
77
B
N
PHE
84
B
N
PHE
84
B
O
VAL
92
B
O
VAL
92
B
N
TRP
97
B
N
TRP
97
B
O
GLY
116
B
O
GLY
116
B
O
THR
121
B
O
THR
121
B
N
THR
11
B
N
THR
11
C
N
TRP
10
C
N
TRP
10
C
O
MET
18
C
O
MET
18
C
N
ASN
17
C
N
ASN
17
C
O
ILE
34
C
O
ILE
34
C
N
TYR
33
C
N
TYR
33
C
O
SER
47
C
O
SER
47
C
N
HIS
50
C
N
HIS
50
C
O
THR
67
C
O
THR
67
C
N
VAL
68
C
N
VAL
68
C
O
THR
77
C
O
THR
77
C
N
GLN
82
C
N
GLN
82
C
O
LYS
94
C
O
LYS
94
C
N
LEU
99
C
N
LEU
99
C
O
ARG
114
C
O
ARG
114
C
O
THR
121
C
O
THR
121
C
N
THR
11
C
N
THR
11
D
N
GLY
8
D
N
GLY
8
D
O
ILE
20
D
O
ILE
20
D
N
ASN
17
D
N
ASN
17
D
O
ILE
34
D
O
ILE
34
D
N
PHE
29
D
N
PHE
29
D
O
GLY
51
D
O
GLY
51
D
N
HIS
50
D
N
HIS
50
D
O
THR
67
D
O
THR
67
D
N
VAL
68
D
N
VAL
68
D
O
THR
77
D
O
THR
77
D
N
THR
76
D
N
THR
76
D
O
ARG
100
D
O
ARG
100
D
N
LEU
93
D
N
LEU
93
D
O
PHE
120
D
O
PHE
120
D
O
THR
121
D
O
THR
121
D
N
THR
11
D
N
THR
11
1
C
CG
ASN
42
C
CG
ASN
42
1
Y
1
C
OD1
ASN
42
C
OD1
ASN
42
1
Y
1
C
ND2
ASN
42
C
ND2
ASN
42
1
Y
1
B
ALA
1
B
ALA
1
1
Y
1
B
ARG
2
B
ARG
2
1
Y
1
D
ALA
1
D
ALA
1
1
Y
1
D
ARG
2
D
ARG
2
1
Y
1
C
C
ND2
C2
ASN
NAG
17
1125
2.13
1
3.52
0.50
120.30
123.82
C
C
C
NE
CZ
NH1
ARG
ARG
ARG
59
59
59
N
1
A
ARG
2
-49.70
154.34
1
A
ASN
12
-125.31
-167.62
1
A
SER
41
-113.87
75.59
1
A
ASN
57
57.95
10.70
1
A
GLN
61
-118.12
74.62
1
A
PHE
72
-140.10
31.82
1
A
ASP
109
-37.64
-37.85
1
B
ASN
57
45.93
14.47
1
C
ILE
106
-58.51
-6.69
88.950
31.883
6.410
-0.0200
0.0000
-0.0900
-0.0500
0.0000
-0.0200
0.9400
0.8970
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.26042
0.19993
0.20297
2.2600
36.7600
1578
29633
5.1000
99.3300
1.000
1.000
6.361
0.158
RANDOM
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.256
0.223
0.8000
0.8000
1.4000
1AVD
MAXIMUM LIKELIHOOD
MASK
2.2600
36.7600
123
4102
158
0
3821
0.023
0.022
4053
2.206
1.963
5502
7.520
5.000
484
35.198
23.846
169
18.714
15.000
673
25.533
15.000
26
0.130
0.200
636
0.010
0.020
2994
1.279
1.500
2412
2.329
2.000
3921
3.454
3.000
1641
5.115
4.500
1581
0.319
0.271
2.317
96
1996
20
92.16
2.25
50
3VHH
31246
1.0
1
100
0.096
2.25
7.7
31246
1
4.2
100
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
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 reduction
HKL-2000
data scaling
HKL-2000
phasing
MOLREP
Crystal structure of DiMe-biotin-avidin complex
1
N
N
1
N
N
1
N
N
1
N
N
2
N
N
3
N
N
4
N
N
4
N
N
2
N
N
3
N
N
4
N
N
2
N
N
3
N
N
4
N
N
4
N
N
2
N
N
3
N
N
4
N
N
5
N
N
5
N
N
5
N
N
5
N
N
A
THR
55
A
THR
55
HELX_P
A
ARG
59
A
ARG
59
5
1
5
A
ASP
105
A
ASP
105
HELX_P
A
LYS
111
A
LYS
111
5
2
7
B
THR
55
B
THR
55
HELX_P
B
ARG
59
B
ARG
59
5
3
5
B
ASP
105
B
ASP
105
HELX_P
B
LYS
111
B
LYS
111
5
4
7
C
THR
55
C
THR
55
HELX_P
C
ARG
59
C
ARG
59
5
5
5
C
ASP
105
C
ASP
105
HELX_P
C
LYS
111
C
LYS
111
5
6
7
D
THR
55
D
THR
55
HELX_P
D
ARG
59
D
ARG
59
5
7
5
D
ASP
105
D
ASP
105
HELX_P
D
LYS
111
D
LYS
111
5
8
7
disulf
2.053
A
CYS
4
A
SG
CYS
4
1_555
A
CYS
83
A
SG
CYS
83
1_555
disulf
2.046
B
CYS
4
B
SG
CYS
4
1_555
B
CYS
83
B
SG
CYS
83
1_555
disulf
2.034
C
CYS
4
C
SG
CYS
4
1_555
C
CYS
83
C
SG
CYS
83
1_555
disulf
2.085
D
CYS
4
D
SG
CYS
4
1_555
D
CYS
83
D
SG
CYS
83
1_555
covale
1.738
one
N-Glycosylation
A
ASN
17
A
ND2
ASN
17
1_555
A
NAG
1125
F
C1
NAG
1_555
covale
1.604
one
N-Glycosylation
B
ASN
17
B
ND2
ASN
17
1_555
B
NAG
1125
J
C1
NAG
1_555
covale
1.616
one
N-Glycosylation
C
ASN
17
C
ND2
ASN
17
1_555
C
NAG
1125
M
C1
NAG
1_555
covale
1.867
one
N-Glycosylation
D
ASN
17
D
ND2
ASN
17
1_555
D
NAG
1125
Q
C1
NAG
1_555
BIOTIN-BINDING PROTEIN
beta barrel, BIOTIN-BINDING PROTEIN
AVID_CHICK
UNP
1
25
P02701
ARKCSLTGKWTNDLGSNMTIGAVNSRGEFTGTYITAVTATSNEIKESPLHGTQNTINKRTQPTFGFTVNWKFSESTTVFT
GQCFIDRNGKEVLKTMWLLRSSVNDIGDDWKATRVGINIFTRL
25
147
3VHH
1
123
P02701
A
1
1
123
25
147
3VHH
1
123
P02701
B
1
1
123
25
147
3VHH
1
123
P02701
C
1
1
123
25
147
3VHH
1
123
P02701
D
1
1
123
9
9
9
9
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
GLY
8
A
GLY
8
A
THR
11
A
THR
11
A
ASN
17
A
ASN
17
A
ILE
20
A
ILE
20
A
GLU
28
A
GLU
28
A
ILE
34
A
ILE
34
A
SER
47
A
SER
47
A
GLN
53
A
GLN
53
A
THR
63
A
THR
63
A
ASN
69
A
ASN
69
A
THR
76
A
THR
76
A
ILE
85
A
ILE
85
A
GLU
91
A
GLU
91
A
ARG
100
A
ARG
100
A
THR
113
A
THR
113
A
ARG
122
A
ARG
122
A
GLY
8
A
GLY
8
A
THR
11
A
THR
11
B
GLY
8
B
GLY
8
B
THR
11
B
THR
11
B
ASN
17
B
ASN
17
B
ILE
20
B
ILE
20
B
GLU
28
B
GLU
28
B
ILE
34
B
ILE
34
B
SER
47
B
SER
47
B
GLN
53
B
GLN
53
B
THR
63
B
THR
63
B
ASN
69
B
ASN
69
B
THR
76
B
THR
76
B
ILE
85
B
ILE
85
B
GLU
91
B
GLU
91
B
ARG
100
B
ARG
100
B
THR
113
B
THR
113
B
ARG
122
B
ARG
122
B
GLY
8
B
GLY
8
B
THR
11
B
THR
11
C
GLY
8
C
GLY
8
C
THR
11
C
THR
11
C
ASN
17
C
ASN
17
C
ILE
20
C
ILE
20
C
GLU
28
C
GLU
28
C
ILE
34
C
ILE
34
C
SER
47
C
SER
47
C
GLN
53
C
GLN
53
C
THR
63
C
THR
63
C
ASN
69
C
ASN
69
C
THR
76
C
THR
76
C
ILE
85
C
ILE
85
C
GLU
91
C
GLU
91
C
ARG
100
C
ARG
100
C
THR
113
C
THR
113
C
ARG
122
C
ARG
122
C
GLY
8
C
GLY
8
C
THR
11
C
THR
11
D
GLY
8
D
GLY
8
D
THR
11
D
THR
11
D
ASN
17
D
ASN
17
D
ILE
20
D
ILE
20
D
GLU
28
D
GLU
28
D
ILE
34
D
ILE
34
D
SER
47
D
SER
47
D
GLN
53
D
GLN
53
D
THR
63
D
THR
63
D
VAL
68
D
VAL
68
D
THR
76
D
THR
76
D
ILE
85
D
ILE
85
D
GLU
91
D
GLU
91
D
ARG
100
D
ARG
100
D
THR
113
D
THR
113
D
ARG
122
D
ARG
122
D
GLY
8
D
GLY
8
D
THR
11
D
THR
11
5
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