0.011362
0.000000
0.003952
0.000000
0.039714
0.000000
0.000000
0.000000
0.027351
0.00000
0.00000
0.00000
Economou, N.J.
Weeks, S.D.
Grasty, K.C.
Loll, P.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
109.18
90.00
88.010
25.180
38.710
C8 H9 N O4
183.161
(2S)-amino(3,5-dihydroxyphenyl)ethanoic acid
L-peptide linking
C9 H10 Cl N O3
215.634
n
3-chloro-D-tyrosine
D-peptide 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
C5 H9 N O4 S
179.194
n
CARBOXYMETHYLATED CYSTEINE
L-peptide linking
C3 H7 N O2
89.093
D-ALANINE
D-peptide linking
C6 H13 N O5
179.171
2-amino-2-deoxy-beta-D-glucopyranose
beta-D-glucosamine; 2-amino-2-deoxy-beta-D-glucose; 2-amino-2-deoxy-D-glucose; 2-amino-2-deoxy-glucose; D-GLUCOSAMINE
D-saccharide, beta linking
C8 H9 N O3
167.162
(2R)-amino(4-hydroxyphenyl)ethanoic acid
D-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
C6 H12 O6
180.156
alpha-D-mannopyranose
alpha-D-mannose; D-mannose; mannose
D-saccharide, alpha 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 O4
197.188
n
(betaR)-beta-hydroxy-L-Tyrosine
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
C10 H20 O2
172.265
8-METHYLNONANOIC ACID
non-polymer
C4 H9 N O3
119.119
y
THREONINE
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
N
O
Y
3
N
C
Y
4
N
C
Y
5
N
C
Y
6
N
C
N
7
N
O
Y
8
N
C
Y
9
N
C
N
10
S
C
N
11
N
C
N
12
N
O
N
13
N
O
N
14
N
H
N
15
N
H
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
O
Y
24
N
C
Y
25
N
C
Y
26
N
C
N
27
N
CL
Y
28
N
C
Y
29
N
C
Y
30
N
C
N
31
N
C
N
32
R
C
N
33
N
C
N
34
N
O
N
35
N
N
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
H
N
45
N
H
N
46
N
H
N
47
N
N
N
48
S
C
N
49
N
C
N
50
N
O
N
51
N
C
N
52
N
O
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
H
N
59
N
H
N
60
N
N
N
61
S
C
N
62
N
C
N
63
N
O
N
64
N
C
N
65
N
C
N
66
N
C
N
67
N
N
N
68
N
C
N
69
N
N
N
70
N
N
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
H
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
N
N
88
S
C
N
89
N
C
N
90
N
O
N
91
N
C
N
92
N
C
N
93
N
O
N
94
N
N
N
95
N
O
N
96
N
H
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
S
C
N
106
N
C
N
107
N
O
N
108
N
C
N
109
N
C
N
110
N
O
N
111
N
O
N
112
N
O
N
113
N
H
N
114
N
H
N
115
N
H
N
116
N
H
N
117
N
H
N
118
N
H
N
119
N
H
N
120
N
N
N
121
R
C
N
122
N
C
N
123
N
S
N
124
N
C
N
125
N
C
N
126
N
O
N
127
N
O
N
128
N
C
N
129
N
O
N
130
N
O
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
N
N
141
R
C
N
142
N
C
N
143
N
C
N
144
N
O
N
145
N
O
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
R
C
N
154
R
C
N
155
R
C
N
156
S
C
N
157
R
C
N
158
N
C
N
159
N
N
N
160
N
O
N
161
N
O
N
162
N
O
N
163
N
O
N
164
N
O
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
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
N
N
179
R
C
N
180
N
C
N
181
N
O
N
182
N
O
Y
183
N
C
Y
184
N
C
Y
185
N
C
Y
186
N
C
N
187
N
O
Y
188
N
C
Y
189
N
C
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
H
N
199
N
N
N
200
S
C
N
201
N
C
N
202
N
O
N
203
N
C
N
204
N
C
N
205
N
C
N
206
N
O
N
207
N
N
N
208
N
O
N
209
N
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
N
N
220
S
C
N
221
N
C
N
222
N
O
N
223
N
C
N
224
N
C
N
225
N
C
N
226
N
O
N
227
N
O
N
228
N
O
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
H
N
236
N
H
N
237
N
H
N
238
N
N
N
239
N
C
N
240
N
C
N
241
N
O
N
242
N
O
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
N
N
249
S
C
N
250
N
C
N
251
N
O
N
252
N
C
Y
253
N
C
Y
254
N
N
Y
255
N
C
Y
256
N
C
Y
257
N
N
N
258
N
O
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
O
N
270
N
H
N
271
N
H
N
272
N
N
N
273
S
C
N
274
N
C
N
275
N
O
N
276
S
C
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
H
N
291
N
H
N
292
N
H
N
293
N
H
N
294
N
N
N
295
S
C
N
296
N
C
N
297
N
O
N
298
N
C
N
299
N
C
N
300
N
C
N
301
N
C
N
302
N
O
N
303
N
H
N
304
N
H
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
C
N
324
N
N
N
325
N
O
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
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
H
N
340
N
H
N
341
S
C
N
342
S
C
N
343
S
C
N
344
S
C
N
345
R
C
N
346
N
C
N
347
N
O
N
348
N
O
N
349
N
O
N
350
N
O
N
351
N
O
N
352
N
O
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
H
N
364
N
H
N
365
N
N
N
366
S
C
N
367
N
C
N
368
N
O
N
369
N
C
N
370
N
C
N
371
N
S
N
372
N
C
N
373
N
O
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
H
N
384
N
H
N
385
R
C
N
386
R
C
N
387
R
C
N
388
S
C
N
389
R
C
N
390
N
C
N
391
N
C
N
392
N
C
N
393
N
N
N
394
N
O
N
395
N
O
N
396
N
O
N
397
N
O
N
398
N
O
N
399
N
O
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
H
N
409
N
H
N
410
N
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
N
N
416
S
C
N
417
N
C
N
418
N
O
N
419
R
C
N
420
N
O
Y
421
N
C
Y
422
N
C
Y
423
N
C
Y
424
N
C
Y
425
N
C
Y
426
N
C
N
427
N
O
N
428
N
O
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
H
N
433
N
H
N
434
N
H
N
435
N
H
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
N
N
441
S
C
N
442
N
C
N
443
N
O
N
444
N
C
Y
445
N
C
Y
446
N
C
Y
447
N
C
Y
448
N
C
Y
449
N
C
Y
450
N
C
N
451
N
O
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
N
N
464
S
C
N
465
N
C
N
466
N
O
N
467
N
C
N
468
N
C
N
469
N
C
N
470
N
O
N
471
N
H
N
472
N
H
N
473
N
H
N
474
N
H
N
475
N
H
N
476
N
H
N
477
N
H
N
478
N
H
N
479
N
H
N
480
N
N
N
481
S
C
N
482
N
C
N
483
N
O
N
484
N
C
N
485
N
O
N
486
N
O
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
H
N
491
N
H
N
492
N
H
N
493
N
H
N
494
N
C
N
495
N
C
N
496
N
C
N
497
N
C
N
498
N
C
N
499
N
C
N
500
N
C
N
501
N
C
N
502
N
C
N
503
N
C
N
504
N
O
N
505
N
O
N
506
N
H
N
507
N
H
N
508
N
H
N
509
N
H
N
510
N
H
N
511
N
H
N
512
N
H
N
513
N
H
N
514
N
H
N
515
N
H
N
516
N
H
N
517
N
H
N
518
N
H
N
519
N
H
N
520
N
H
N
521
N
H
N
522
N
H
N
523
N
H
N
524
N
H
N
525
N
H
N
526
N
N
N
527
S
C
N
528
N
C
N
529
N
O
N
530
R
C
N
531
N
O
N
532
N
C
N
533
N
O
N
534
N
H
N
535
N
H
N
536
N
H
N
537
N
H
N
538
N
H
N
539
N
H
N
540
N
H
N
541
N
H
N
542
N
H
N
543
N
N
N
544
S
C
N
545
N
C
N
546
N
O
N
547
N
C
Y
548
N
C
Y
549
N
C
Y
550
N
C
Y
551
N
C
Y
552
N
C
Y
553
N
C
N
554
N
O
N
555
N
O
N
556
N
H
N
557
N
H
N
558
N
H
N
559
N
H
N
560
N
H
N
561
N
H
N
562
N
H
N
563
N
H
N
564
N
H
N
565
N
H
N
566
N
H
N
567
N
N
N
568
S
C
N
569
N
C
N
570
N
O
N
571
N
C
N
572
N
C
N
573
N
C
N
574
N
O
N
575
N
H
N
576
N
H
N
577
N
H
N
578
N
H
N
579
N
H
N
580
N
H
N
581
N
H
N
582
N
H
N
583
N
H
N
584
N
H
N
585
N
H
N
1
N
sing
N
2
N
sing
Y
3
N
sing
Y
4
N
doub
Y
5
N
doub
Y
6
N
sing
N
7
N
sing
Y
8
N
doub
Y
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
doub
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
Y
24
N
sing
Y
25
N
doub
Y
26
N
doub
N
27
N
sing
Y
28
N
sing
Y
29
N
sing
Y
30
N
doub
N
31
N
sing
N
32
N
sing
N
33
N
sing
N
34
N
sing
N
35
N
doub
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
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
doub
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
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
sing
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
doub
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
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
sing
N
107
N
doub
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
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
sing
N
129
N
doub
N
130
N
sing
N
131
N
sing
N
132
N
doub
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
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
doub
N
145
N
sing
N
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
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
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
doub
N
179
N
sing
N
180
N
sing
Y
181
N
doub
Y
182
N
sing
Y
183
N
sing
N
184
N
sing
Y
185
N
doub
N
186
N
sing
N
187
N
sing
Y
188
N
sing
N
189
N
sing
Y
190
N
doub
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
doub
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
doub
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
doub
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
doub
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
doub
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
Y
250
N
sing
Y
251
N
doub
Y
252
N
doub
N
253
N
sing
Y
254
N
sing
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
sing
N
267
N
sing
N
268
N
doub
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
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
sing
N
289
N
doub
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
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
doub
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
sing
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
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
sing
N
347
N
sing
N
348
N
sing
N
349
N
sing
N
350
N
sing
N
351
N
sing
N
352
N
sing
N
353
N
sing
N
354
N
sing
N
355
N
sing
N
356
N
sing
N
357
N
sing
N
358
N
doub
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
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
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
doub
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
doub
N
405
N
sing
N
406
N
sing
N
407
N
sing
Y
408
N
sing
Y
409
N
doub
Y
410
N
doub
Y
411
N
sing
Y
412
N
sing
Y
413
N
doub
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
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
sing
N
429
N
sing
N
430
N
sing
N
431
N
sing
N
432
N
doub
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
Y
437
N
doub
Y
438
N
sing
Y
439
N
sing
N
440
N
sing
Y
441
N
doub
N
442
N
sing
Y
443
N
doub
N
444
N
sing
Y
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
N
449
N
sing
N
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
doub
N
456
N
sing
N
457
N
sing
N
458
N
sing
N
459
N
sing
N
460
N
sing
N
461
N
sing
N
462
N
sing
N
463
N
sing
N
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
sing
N
468
N
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
doub
N
473
N
sing
N
474
N
sing
N
475
N
sing
N
476
N
sing
N
477
N
sing
N
478
N
sing
N
479
N
sing
N
480
N
sing
N
481
N
sing
N
482
N
doub
N
483
N
sing
N
484
N
sing
N
485
N
sing
N
486
N
sing
N
487
N
sing
N
488
N
sing
N
489
N
sing
N
490
N
sing
N
491
N
sing
N
492
N
sing
N
493
N
sing
N
494
N
sing
N
495
N
sing
N
496
N
sing
N
497
N
sing
N
498
N
sing
N
499
N
sing
N
500
N
sing
N
501
N
sing
N
502
N
sing
N
503
N
sing
N
504
N
sing
N
505
N
sing
N
506
N
sing
N
507
N
sing
N
508
N
sing
N
509
N
sing
N
510
N
sing
N
511
N
sing
N
512
N
sing
N
513
N
sing
N
514
N
sing
N
515
N
sing
N
516
N
doub
N
517
N
sing
N
518
N
sing
N
519
N
sing
N
520
N
sing
N
521
N
sing
N
522
N
sing
N
523
N
sing
N
524
N
sing
N
525
N
sing
N
526
N
sing
N
527
N
sing
N
528
N
sing
N
529
N
sing
N
530
N
sing
N
531
N
sing
N
532
N
doub
N
533
N
sing
N
534
N
sing
N
535
N
sing
N
536
N
sing
Y
537
N
doub
Y
538
N
sing
Y
539
N
sing
N
540
N
sing
Y
541
N
doub
N
542
N
sing
Y
543
N
doub
N
544
N
sing
Y
545
N
sing
N
546
N
sing
N
547
N
sing
N
548
N
sing
N
549
N
sing
N
550
N
sing
N
551
N
sing
N
552
N
sing
N
553
N
sing
N
554
N
sing
N
555
N
sing
N
556
N
doub
N
557
N
sing
N
558
N
sing
N
559
N
sing
N
560
N
sing
N
561
N
sing
N
562
N
sing
N
563
N
sing
N
564
N
sing
N
565
N
sing
N
566
N
sing
N
567
N
sing
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
69
520
533
10.1107/S0907444912050469
23519660
Structure of the complex between teicoplanin and a bacterial cell-wall peptide: use of a carrier-protein approach.
2013
10.2210/pdb3vfk/pdb
pdb_00003vfk
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
93
1
CCD
2009-04-10
ADSC QUANTUM 315
Cryogenically-cooled single crystal Si(111)side bounce monochromator
SINGLE WAVELENGTH
M
x-ray
1
0.9792
1.0
24-ID-E
APS
0.9792
SYNCHROTRON
APS BEAMLINE 24-ID-E
8952.293
ubiquitin, C-terminal fused by Cys-Lys-D-Ala-D-Ala
1
man
polymer
1172.539
MonodeChloro- Teicoplanin A2-2
1
nat
polymer
179.171
2-amino-2-deoxy-beta-D-glucopyranose
1
man
non-polymer
172.265
8-METHYLNONANOIC ACID
1
syn
non-polymer
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
1
man
non-polymer
180.156
alpha-D-mannopyranose
1
man
non-polymer
18.015
water
10
nat
water
Ubiquitin
no
yes
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG(CCS)
K(DAL)(DAL)
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGCKAA
A
polypeptide(L)
no
yes
(GHP)(3MY)(3FG)(GHP)(GHP)(OMX)(3FG)
GYXGGYX
G
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
human
four C-terminal amino acids added non-recombinantly with native chemical ligation
sample
UBC
9606
Homo sapiens
562
Escherichia coli
sample
1867
Actinoplanes teichomyceticus
2
2.00
38.42
VAPOR DIFFUSION, HANGING DROP
4.6
0.1 M magnesium chloride, 0.1 M sodium acetate 4.6, 18% PEG 1500, VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
chem_comp
entity
entity_poly
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
entity_poly
chem_comp_atom
chem_comp_bond
struct_conn
repository
Initial release
Carbohydrate remediation
repository
Remediation
Structure summary
Derived calculations
Database references
Data collection
Derived calculations
Polymer sequence
Structure summary
Data collection
Database references
Refinement description
Structure summary
Polymer sequence
Data collection
Derived calculations
1
0
2013-01-09
1
1
2013-03-27
1
2
2013-04-03
1
3
2013-06-19
2
0
2020-07-29
2
1
2023-09-13
3
0
2023-09-27
3
1
2023-12-06
_chem_comp.name
_chem_comp.type
_entity.pdbx_description
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_entity_nonpoly.name
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_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
_entity_poly.type
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_2
_struct_conn.pdbx_leaving_atom_flag
DGlcpNb
b-D-glucopyranosamine
b-D-GlcpN
GlcN
DManpa
a-D-mannopyranose
a-D-Manp
Man
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
Native MBP structure used for molecular replacement
same crystallographic strategy: vancomycin bound to a T4 lysozyme-substrate fusion
same crystallographic strategy: dalbavancin bound to the same ubiquitin fusion
same crystallographic strategy: ristocetin bound to a MBP-substrate fusion
The structure of monodechloro-teicoplanin in complex with its ligand, using MBP as a ligand
RCSB
Y
RCSB
2012-01-09
REL
REL
GCS
2-amino-2-deoxy-beta-D-glucopyranose
T55
8-METHYLNONANOIC ACID
NAG
2-acetamido-2-deoxy-beta-D-glucopyranose
MAN
alpha-D-mannopyranose
HOH
water
AUTHORS STATED THE FOLLOWING: THE STARTING MATERIAL HAD TEICOPLANIN A2-2 THAT CONTAINED TWO CHLORINE ATOMS. THE ACTUAL CRYSTALS CONTAINED BOTH CHLORINE ATOMS BEFORE THEY WERE EXPOSED TO X-RAYS. ONE CHLORINE WAS REMOVED FROM TEICOPLANIN BY X-IRRADIATION DAMAGE EARLY IN THE DIFFRACTION EXPERIMENT
TEICOPLANIN IS A FAMILY OF TETRACYCLIC GLYCOPEPTIDE ANTIBIOTICS. THE SCAFFOLD IS A HEPTAPEPTIDE FURTHER GLYCOSYLATED BY THREE MONO SACCHARIDES: MANNOSE, N-ACETYLGLUCOSAMINE AND BETA-D-GLUCOSAMINE AND ONLY DIFFER BY THE SIDE CHAIN ATTACHED TO THE LATTER. TEICOPLANIN A2-2 HAS 8-METHYLNONANOIC ACID ATTACHED TO GLUCOSAMINE. HERE, TEICOPLANIN A2-2 WAS UNDER RADIATION DAMAGE, WHICH CAUSES THE LOSS OF ONE CHLORINE ATOM.
C-TERMINAL FUSED BY MODIFIED CYS-LYS-D-ALA-D-ALA
1UBQ
PDB entry 1UBQ
PDB
experimental model
Antibiotic
MonodeChloro- Teicoplanin A2-2
Glycopeptide
GCS
8
3
GCS
GCS
8
G
T55
9
4
T55
T55
9
G
NAG
10
5
NAG
NAG
10
G
MAN
11
6
MAN
MAN
11
G
HOH
1
7
HOH
HOH
201
A
HOH
2
7
HOH
HOH
202
A
HOH
3
7
HOH
HOH
203
A
HOH
4
7
HOH
HOH
204
A
HOH
5
7
HOH
HOH
205
A
HOH
6
7
HOH
HOH
206
A
HOH
7
7
HOH
HOH
207
A
HOH
8
7
HOH
HOH
208
A
HOH
9
7
HOH
HOH
209
A
HOH
10
7
HOH
HOH
210
A
MET
1
n
1
MET
1
A
GLN
2
n
2
GLN
2
A
ILE
3
n
3
ILE
3
A
PHE
4
n
4
PHE
4
A
VAL
5
n
5
VAL
5
A
LYS
6
n
6
LYS
6
A
THR
7
n
7
THR
7
A
LEU
8
n
8
LEU
8
A
THR
9
n
9
THR
9
A
GLY
10
n
10
GLY
10
A
LYS
11
n
11
LYS
11
A
THR
12
n
12
THR
12
A
ILE
13
n
13
ILE
13
A
THR
14
n
14
THR
14
A
LEU
15
n
15
LEU
15
A
GLU
16
n
16
GLU
16
A
VAL
17
n
17
VAL
17
A
GLU
18
n
18
GLU
18
A
PRO
19
n
19
PRO
19
A
SER
20
n
20
SER
20
A
ASP
21
n
21
ASP
21
A
THR
22
n
22
THR
22
A
ILE
23
n
23
ILE
23
A
GLU
24
n
24
GLU
24
A
ASN
25
n
25
ASN
25
A
VAL
26
n
26
VAL
26
A
LYS
27
n
27
LYS
27
A
ALA
28
n
28
ALA
28
A
LYS
29
n
29
LYS
29
A
ILE
30
n
30
ILE
30
A
GLN
31
n
31
GLN
31
A
ASP
32
n
32
ASP
32
A
LYS
33
n
33
LYS
33
A
GLU
34
n
34
GLU
34
A
GLY
35
n
35
GLY
35
A
ILE
36
n
36
ILE
36
A
PRO
37
n
37
PRO
37
A
PRO
38
n
38
PRO
38
A
ASP
39
n
39
ASP
39
A
GLN
40
n
40
GLN
40
A
GLN
41
n
41
GLN
41
A
ARG
42
n
42
ARG
42
A
LEU
43
n
43
LEU
43
A
ILE
44
n
44
ILE
44
A
PHE
45
n
45
PHE
45
A
ALA
46
n
46
ALA
46
A
GLY
47
n
47
GLY
47
A
LYS
48
n
48
LYS
48
A
GLN
49
n
49
GLN
49
A
LEU
50
n
50
LEU
50
A
GLU
51
n
51
GLU
51
A
ASP
52
n
52
ASP
52
A
GLY
53
n
53
GLY
53
A
ARG
54
n
54
ARG
54
A
THR
55
n
55
THR
55
A
LEU
56
n
56
LEU
56
A
SER
57
n
57
SER
57
A
ASP
58
n
58
ASP
58
A
TYR
59
n
59
TYR
59
A
ASN
60
n
60
ASN
60
A
ILE
61
n
61
ILE
61
A
GLN
62
n
62
GLN
62
A
LYS
63
n
63
LYS
63
A
GLU
64
n
64
GLU
64
A
SER
65
n
65
SER
65
A
THR
66
n
66
THR
66
A
LEU
67
n
67
LEU
67
A
HIS
68
n
68
HIS
68
A
LEU
69
n
69
LEU
69
A
VAL
70
n
70
VAL
70
A
LEU
71
n
71
LEU
71
A
ARG
72
n
72
ARG
72
A
LEU
73
n
73
LEU
73
A
ARG
74
n
74
ARG
74
A
GLY
75
n
75
GLY
75
A
CCS
76
n
76
CCS
76
A
LYS
77
n
77
LYS
77
A
DAL
78
n
78
DAL
78
A
DAL
79
n
79
DAL
79
A
NTR
1
n
1
GHP
1
G
3MY
2
n
2
3MY
2
G
3FG
3
n
3
3FG
3
G
GHP
4
n
4
GHP
4
G
GHP
5
n
5
GHP
5
G
OMX
6
n
6
OMX
6
G
3FG
7
n
7
3FG
7
G
author_defined_assembly
2
dimeric
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
O
LEU
15
A
O
LEU
15
A
N
ILE
3
A
N
ILE
3
A
N
PHE
4
A
N
PHE
4
A
O
LEU
67
A
O
LEU
67
A
O
HIS
68
A
O
HIS
68
A
N
ILE
44
A
N
ILE
44
A
N
PHE
45
A
N
PHE
45
A
O
LYS
48
A
O
LYS
48
1
A
ARG
54
-175.15
127.86
1
G
3FG
3
-143.02
-67.54
8.4159
0.0000
-18.7315
-20.2601
-0.0000
11.8442
0.3057
0.2776
0.2789
2.800
19.294
93
2084
4.46
99.95
0.45
1
2.04
MOLECULAR REPLACEMENT
34.93
0.00
0.30
PDB entry 1UBQ
ML
FLAT BULK SOLVENT MODEL
77.331
0.424
2.800
19.294
10
768
47
0
711
0.005
777
0.847
1061
12.765
318
0.037
122
0.004
132
2.8
19.294
3VFK
2084
-3
1
99.2
phasing
MOLREP
refinement
PHENIX
(phenix.refine: 1.6.2_432)
data reduction
XDS
data scaling
XSCALE
The structure of monodechloro-teicoplanin in complex with its ligand, using ubiquitin as a ligand carrier
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
6
N
N
7
N
N
A
THR
22
A
THR
22
HELX_P
A
GLU
34
A
GLU
34
1
1
13
A
PRO
37
A
PRO
37
HELX_P
A
ASP
39
A
ASP
39
5
2
3
A
LEU
56
A
LEU
56
HELX_P
A
ASN
60
A
ASN
60
5
3
5
covale
1.323
both
A
GLY
75
A
C
GLY
75
1_555
A
CCS
76
A
N
CCS
76
1_555
covale
1.332
both
A
CCS
76
A
C
CCS
76
1_555
A
LYS
77
A
N
LYS
77
1_555
covale
1.326
both
A
LYS
77
A
C
LYS
77
1_555
A
DAL
78
A
N
DAL
78
1_555
covale
1.326
both
A
DAL
78
A
C
DAL
78
1_555
A
DAL
79
A
N
DAL
79
1_555
covale
1.330
both
G
GHP
1
B
C
GHP
1
1_555
G
3MY
2
B
N
3MY
2
1_555
covale
1.362
none
G
GHP
1
B
C5
GHP
1
1_555
G
3FG
3
B
OD1
3FG
3
1_555
covale
1.331
both
G
3MY
2
B
C
3MY
2
1_555
G
3FG
3
B
N
3FG
3
1_555
covale
1.383
one
G
3MY
2
B
OBD
3MY
2
1_555
G
GHP
4
B
C3
GHP
4
1_555
covale
1.330
one
G
3FG
3
B
C
3FG
3
1_555
G
GHP
4
B
N
GHP
4
1_555
covale
1.331
both
G
GHP
4
B
C
GHP
4
1_555
G
GHP
5
B
N
GHP
5
1_555
covale
1.384
none
G
GHP
4
B
C5
GHP
4
1_555
G
OMX
6
B
OH
OMX
6
1_555
covale
1.383
one
G
GHP
4
B
O4
GHP
4
1_555
G
GCS
8
C
C1
GCS
1_555
covale
1.328
both
G
GHP
5
B
C
GHP
5
1_555
G
OMX
6
B
N
OMX
6
1_555
covale
1.399
one
G
GHP
5
B
C3
GHP
5
1_555
G
3FG
7
B
CG1
3FG
7
1_555
covale
1.328
both
G
OMX
6
B
C
OMX
6
1_555
G
3FG
7
B
N
3FG
7
1_555
covale
1.384
one
G
OMX
6
B
OC
OMX
6
1_555
G
NAG
10
E
C1
NAG
1_555
covale
1.422
one
G
3FG
7
B
OD1
3FG
7
1_555
G
MAN
11
F
C1
MAN
1_555
covale
1.462
both
G
GCS
8
C
N2
GCS
1_555
G
T55
9
D
C
T55
1_555
SUGAR BINDING PROTEIN/ANTIBIOTIC
teicoplanin, acetylation of cyteine with iodoacetate modification, SUGAR BINDING PROTEIN-ANTIBIOTIC complex
G
GHP
5
B
GHP
5
1
G
OMX
6
B
OMX
6
1.18
UBC_HUMAN
UNP
1
1
P0CG48
MQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRG
3VFK
PDB
2
3VFK
1
75
3VFK
1
75
P0CG48
A
1
1
75
1
7
3VFK
1
7
3VFK
G
2
1
7
1
SEE REMARK 999
CCS
76
3VFK
A
P0CG48
UNP
76
1
SEE REMARK 999
LYS
77
3VFK
A
P0CG48
UNP
77
1
SEE REMARK 999
DAL
78
3VFK
A
P0CG48
UNP
78
1
SEE REMARK 999
DAL
79
3VFK
A
P0CG48
UNP
79
5
anti-parallel
parallel
anti-parallel
anti-parallel
A
ILE
13
A
ILE
13
A
GLU
16
A
GLU
16
A
GLN
2
A
GLN
2
A
THR
7
A
THR
7
A
SER
65
A
SER
65
A
LEU
71
A
LEU
71
A
GLN
41
A
GLN
41
A
PHE
45
A
PHE
45
A
LYS
48
A
LYS
48
A
GLN
49
A
GLN
49
5
C 1 2 1