0.016545
0.009552
0.000000
0.000000
0.019105
0.000000
0.000000
0.000000
0.010327
0.00000
0.00000
0.00000
Economou, N.J.
Townsend, T.M.
Loll, P.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
60.440
60.440
96.830
C8 H9 N O4
183.161
(2S)-amino(3,5-dihydroxyphenyl)ethanoic acid
L-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
C6 H12 O6
180.156
beta-D-glucopyranose
beta-D-glucose; D-glucose; glucose
D-saccharide, beta linking
C5 H9 N O4 S
179.194
n
CARBOXYMETHYLATED CYSTEINE
L-peptide linking
Cl -1
35.453
CHLORIDE ION
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C3 H7 N O2
89.093
D-ALANINE
D-peptide 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
C3 H8 O
60.095
ISOPROPYL ALCOHOL
2-PROPANOL
non-polymer
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
C7 H15 N O2
145.199
N-methyl-D-leucine
D-peptide linking
C6 H14 O2
118.174
(4S)-2-METHYL-2,4-PENTANEDIOL
non-polymer
C6 H14 O2
118.174
(4R)-2-METHYLPENTANE-2,4-DIOL
non-polymer
C9 H10 Cl N O4
231.633
n
(betaR)-3-chloro-beta-hydroxy-L-tyrosine
L-peptide linking
C9 H10 Cl N O4
231.633
(betaR)-3-CHLORO-BETA-HYDROXY-D-TYROSINE
D-peptide linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
O4 P -3
94.971
PHOSPHATE ION
non-polymer
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C7 H15 N O3
161.199
vancosamine
(1R,3S,4S,5S)-3-amino-2,3,6-trideoxy-3-methyl-alpha-L-arabino-hexopyranose
L-saccharide, alpha 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
C4 H12 N O3 1
122.143
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
TRIS BUFFER
non-polymer
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
N
N
24
S
C
N
25
N
C
N
26
N
O
N
27
N
C
N
28
N
O
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
N
N
37
S
C
N
38
N
C
N
39
N
O
N
40
N
C
N
41
N
C
N
42
N
C
N
43
N
N
N
44
N
C
N
45
N
N
N
46
N
N
N
47
N
O
N
48
N
H
N
49
N
H
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
H
N
59
N
H
N
60
N
H
N
61
N
H
N
62
N
H
N
63
N
N
N
64
S
C
N
65
N
C
N
66
N
O
N
67
N
C
N
68
N
C
N
69
N
O
N
70
N
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
N
N
81
S
C
N
82
N
C
N
83
N
O
N
84
N
C
N
85
N
C
N
86
N
O
N
87
N
O
N
88
N
O
N
89
N
H
N
90
N
H
N
91
N
H
N
92
N
H
N
93
N
H
N
94
N
H
N
95
N
H
N
96
R
C
N
97
S
C
N
98
S
C
N
99
R
C
N
100
N
C
N
101
R
C
N
102
N
O
N
103
N
O
N
104
N
O
N
105
N
O
N
106
N
O
N
107
N
O
N
108
N
H
N
109
N
H
N
110
N
H
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
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
CL
N
141
N
N
N
142
R
C
N
143
N
C
N
144
N
O
N
145
N
C
N
146
N
S
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
N
N
156
R
C
N
157
N
C
N
158
N
C
N
159
N
O
N
160
N
O
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
H
N
168
N
N
N
169
R
C
N
170
N
C
N
171
N
O
N
172
N
O
Y
173
N
C
Y
174
N
C
Y
175
N
C
Y
176
N
C
N
177
N
O
Y
178
N
C
Y
179
N
C
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
N
N
190
S
C
N
191
N
C
N
192
N
O
N
193
N
C
N
194
N
C
N
195
N
C
N
196
N
O
N
197
N
N
N
198
N
O
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
N
N
210
S
C
N
211
N
C
N
212
N
O
N
213
N
C
N
214
N
C
N
215
N
C
N
216
N
O
N
217
N
O
N
218
N
O
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
N
N
229
N
C
N
230
N
C
N
231
N
O
N
232
N
O
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
S
C
N
240
N
C
N
241
N
O
N
242
N
C
Y
243
N
C
Y
244
N
N
Y
245
N
C
Y
246
N
C
Y
247
N
N
N
248
N
O
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
O
N
260
N
H
N
261
N
H
N
262
N
N
N
263
S
C
N
264
N
C
N
265
N
O
N
266
S
C
N
267
N
C
N
268
N
C
N
269
N
C
N
270
N
O
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
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
C
N
285
N
C
N
286
N
C
N
287
N
O
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
H
N
295
N
H
N
296
N
N
N
297
S
C
N
298
N
C
N
299
N
O
N
300
N
C
N
301
N
C
N
302
N
C
N
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
H
N
317
N
H
N
318
N
N
N
319
S
C
N
320
N
C
N
321
N
O
N
322
N
C
N
323
N
C
N
324
N
C
N
325
N
C
N
326
N
N
N
327
N
O
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
N
H
N
342
N
H
N
343
N
N
N
344
S
C
N
345
N
C
N
346
N
O
N
347
N
C
N
348
N
C
N
349
N
S
N
350
N
C
N
351
N
O
N
352
N
H
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
N
N
364
N
C
N
365
R
C
N
366
N
C
N
367
N
O
N
368
N
C
N
369
N
C
N
370
N
C
N
371
N
C
N
372
N
O
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
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
C
N
389
N
C
N
390
N
O
N
391
N
C
N
392
N
C
N
393
S
C
N
394
N
O
N
395
N
C
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
H
N
409
N
H
N
410
N
C
N
411
N
C
N
412
N
O
N
413
N
C
N
414
N
C
N
415
R
C
N
416
N
O
N
417
N
C
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
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
O
Y
435
N
C
Y
436
N
C
Y
437
N
C
Y
438
N
C
Y
439
N
C
Y
440
N
C
N
441
R
C
N
442
N
CL
N
443
N
O
N
444
N
C
N
445
N
O
N
446
N
O
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
N
N
458
R
C
N
459
N
C
N
460
N
O
N
461
N
O
N
462
R
C
N
463
N
O
Y
464
N
C
Y
465
N
C
Y
466
N
C
Y
467
N
C
N
468
N
CL
Y
469
N
C
Y
470
N
C
N
471
N
O
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
H
N
481
N
H
N
482
N
N
N
483
S
C
N
484
N
C
N
485
N
O
N
486
N
C
Y
487
N
C
Y
488
N
C
Y
489
N
C
Y
490
N
C
Y
491
N
C
Y
492
N
C
N
493
N
O
N
494
N
H
N
495
N
H
N
496
N
H
N
497
N
H
N
498
N
H
N
499
N
H
N
500
N
H
N
501
N
H
N
502
N
H
N
503
N
H
N
504
N
H
N
505
N
P
N
506
N
O
N
507
N
O
N
508
N
O
N
509
N
O
N
510
N
N
N
511
S
C
N
512
N
C
N
513
N
O
N
514
N
C
N
515
N
C
N
516
N
C
N
517
N
O
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
H
N
527
R
C
N
528
N
C
N
529
S
C
N
530
N
N
N
531
N
C
N
532
S
C
N
533
N
O
N
534
S
C
N
535
N
O
N
536
N
C
N
537
N
O
N
538
N
H
N
539
N
H
N
540
N
H
N
541
N
H
N
542
N
H
N
543
N
H
N
544
N
H
N
545
N
H
N
546
N
H
N
547
N
H
N
548
N
H
N
549
N
H
N
550
N
H
N
551
N
H
N
552
N
H
N
553
N
N
N
554
S
C
N
555
N
C
N
556
N
O
N
557
N
C
N
558
N
O
N
559
N
O
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
R
C
N
572
N
O
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
N
N
585
S
C
N
586
N
C
N
587
N
O
N
588
N
C
Y
589
N
C
Y
590
N
C
Y
591
N
C
Y
592
N
N
Y
593
N
C
Y
594
N
C
Y
595
N
C
Y
596
N
C
Y
597
N
C
N
598
N
O
N
599
N
H
N
600
N
H
N
601
N
H
N
602
N
H
N
603
N
H
N
604
N
H
N
605
N
H
N
606
N
H
N
607
N
H
N
608
N
H
N
609
N
H
N
610
N
H
N
611
N
C
N
612
N
C
N
613
N
C
N
614
N
C
N
615
N
N
N
616
N
O
N
617
N
O
N
618
N
O
N
619
N
H
N
620
N
H
N
621
N
H
N
622
N
H
N
623
N
H
N
624
N
H
N
625
N
H
N
626
N
H
N
627
N
H
N
628
N
H
N
629
N
H
N
630
N
H
N
631
N
N
N
632
S
C
N
633
N
C
N
634
N
O
N
635
N
C
Y
636
N
C
Y
637
N
C
Y
638
N
C
Y
639
N
C
Y
640
N
C
Y
641
N
C
N
642
N
O
N
643
N
O
N
644
N
H
N
645
N
H
N
646
N
H
N
647
N
H
N
648
N
H
N
649
N
H
N
650
N
H
N
651
N
H
N
652
N
H
N
653
N
H
N
654
N
H
N
655
N
N
N
656
S
C
N
657
N
C
N
658
N
O
N
659
N
C
N
660
N
C
N
661
N
C
N
662
N
O
N
663
N
H
N
664
N
H
N
665
N
H
N
666
N
H
N
667
N
H
N
668
N
H
N
669
N
H
N
670
N
H
N
671
N
H
N
672
N
H
N
673
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
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
doub
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
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
doub
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
sing
N
54
N
sing
N
55
N
doub
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
sing
N
66
N
sing
N
67
N
doub
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
doub
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
doub
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
doub
N
89
N
sing
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
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
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
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
doub
N
142
N
sing
N
143
N
sing
N
144
N
sing
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
doub
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
doub
N
167
N
sing
N
168
N
sing
Y
169
N
doub
Y
170
N
sing
Y
171
N
sing
N
172
N
sing
Y
173
N
doub
N
174
N
sing
N
175
N
sing
Y
176
N
sing
N
177
N
sing
Y
178
N
doub
N
179
N
sing
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
doub
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
doub
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
doub
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
doub
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
doub
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
Y
238
N
sing
Y
239
N
doub
Y
240
N
doub
N
241
N
sing
Y
242
N
sing
N
243
N
sing
Y
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
doub
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
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
sing
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
doub
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
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
doub
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
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
doub
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
doub
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
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
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
sing
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
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
Y
414
N
sing
Y
415
N
doub
Y
416
N
doub
Y
417
N
sing
Y
418
N
doub
N
419
N
sing
Y
420
N
sing
N
421
N
sing
N
422
N
doub
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
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
doub
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
Y
445
N
doub
Y
446
N
sing
Y
447
N
sing
Y
448
N
doub
Y
449
N
doub
Y
450
N
sing
N
451
N
sing
N
452
N
sing
N
453
N
sing
N
454
N
sing
N
455
N
sing
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
doub
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
sing
Y
473
N
doub
Y
474
N
sing
Y
475
N
sing
N
476
N
sing
Y
477
N
doub
N
478
N
sing
Y
479
N
doub
N
480
N
sing
Y
481
N
sing
N
482
N
sing
N
483
N
sing
N
484
N
sing
N
485
N
doub
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
doub
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
sing
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
sing
N
533
N
sing
N
534
N
sing
N
535
N
sing
N
536
N
sing
N
537
N
sing
N
538
N
doub
N
539
N
sing
N
540
N
sing
N
541
N
sing
N
542
N
sing
N
543
N
sing
N
544
N
sing
N
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
doub
N
552
N
sing
N
553
N
sing
N
554
N
sing
N
555
N
sing
N
556
N
sing
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
doub
N
568
N
sing
N
569
N
sing
N
570
N
sing
N
571
N
sing
Y
572
N
doub
Y
573
N
sing
Y
574
N
sing
N
575
N
sing
Y
576
N
doub
Y
577
N
sing
Y
578
N
sing
N
579
N
sing
Y
580
N
sing
Y
581
N
doub
N
582
N
sing
Y
583
N
doub
N
584
N
sing
Y
585
N
sing
N
586
N
sing
N
587
N
sing
N
588
N
sing
N
589
N
sing
N
590
N
sing
N
591
N
sing
N
592
N
sing
N
593
N
sing
N
594
N
sing
N
595
N
sing
N
596
N
sing
N
597
N
sing
N
598
N
sing
N
599
N
sing
N
600
N
sing
N
601
N
sing
N
602
N
sing
N
603
N
sing
N
604
N
sing
N
605
N
sing
N
606
N
sing
N
607
N
sing
N
608
N
sing
N
609
N
sing
N
610
N
sing
N
611
N
sing
N
612
N
sing
N
613
N
sing
N
614
N
doub
N
615
N
sing
N
616
N
sing
N
617
N
sing
N
618
N
sing
Y
619
N
doub
Y
620
N
sing
Y
621
N
sing
N
622
N
sing
Y
623
N
doub
N
624
N
sing
Y
625
N
doub
N
626
N
sing
Y
627
N
sing
N
628
N
sing
N
629
N
sing
N
630
N
sing
N
631
N
sing
N
632
N
sing
N
633
N
sing
N
634
N
sing
N
635
N
sing
N
636
N
sing
N
637
N
sing
N
638
N
doub
N
639
N
sing
N
640
N
sing
N
641
N
sing
N
642
N
sing
N
643
N
sing
N
644
N
sing
N
645
N
sing
N
646
N
sing
N
647
N
sing
N
648
N
sing
N
649
N
sing
US
J.Am.Chem.Soc.
JACSAT
0004
0002-7863
134
4637
4645
10.1021/ja208755j
22352468
A carrier protein strategy yields the structure of dalbavancin.
2012
10.2210/pdb3run/pdb
pdb_00003run
93
1
2011-03-25
SINGLE WAVELENGTH
M
x-ray
1
1.000
1.0
X6A
NSLS
1.000
SYNCHROTRON
NSLS BEAMLINE X6A
19018.799
LYSOZYME
3.2.1.17
C54T, C97A, L164A
1
man
polymer
1149.977
VANCOMYCIN
1
nat
polymer
323.340
vancosamine-(1-2)-beta-D-glucopyranose
1
man
branched
118.174
(4S)-2-METHYL-2,4-PENTANEDIOL
1
syn
non-polymer
118.174
(4R)-2-METHYLPENTANE-2,4-DIOL
2
syn
non-polymer
94.971
PHOSPHATE ION
1
syn
non-polymer
122.143
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
1
syn
non-polymer
35.453
CHLORIDE ION
1
syn
non-polymer
60.095
ISOPROPYL ALCOHOL
2
syn
non-polymer
18.015
water
316
nat
water
Endolysin, Lysis protein, Muramidase
no
yes
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILR
NAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDA
YKNA(CCS)K(DAL)(DAL)
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNTNGVITKDEAEKLFNQDVDAAVRGILR
NAKLKPVYDSLDAVRRAALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDA
YKNACKAA
A
polypeptide(L)
no
yes
(MLU)(OMZ)N(GHP)(GHP)(OMY)(3FG)
XXNGGYX
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
sample
E
10665
ENTEROBACTERIA PHAGE T4
562
ESCHERICHIA COLI
sample
31958
Streptomyces orientalis
1
2.68
54.18
VAPOR DIFFUSION, HANGING DROP
8.5
0.2M ammonium phosphate, 0.1M Tris 8.5, 35% MPD, vapor diffusion, hanging drop, temperature 291K
291
atom_site
chem_comp
entity
entity_poly
pdbx_branch_scheme
pdbx_chem_comp_identifier
pdbx_entity_branch
pdbx_entity_branch_descriptor
pdbx_entity_branch_link
pdbx_entity_branch_list
pdbx_entity_nonpoly
pdbx_molecule
pdbx_nonpoly_scheme
pdbx_struct_assembly_gen
pdbx_struct_special_symmetry
struct_asym
struct_conn
struct_ref_seq_dif
struct_site
struct_site_gen
chem_comp
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
chem_comp_atom
chem_comp_bond
repository
Initial release
Carbohydrate remediation
repository
Remediation
Other
Atomic model
Data collection
Database references
Derived calculations
Polymer sequence
Structure summary
Data collection
Database references
Refinement description
Structure summary
Data collection
1
0
2012-06-06
1
1
2013-02-27
2
0
2020-07-29
2
1
2023-09-13
2
2
2023-12-06
_atom_site.B_iso_or_equiv
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.auth_asym_id
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.label_alt_id
_atom_site.label_asym_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_entity_id
_atom_site.occupancy
_atom_site.type_symbol
_chem_comp.name
_chem_comp.type
_entity_poly.pdbx_seq_one_letter_code_can
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_special_symmetry.label_asym_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_ptnr1_label_alt_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.ptnr1_label_seq_id
_struct_conn.ptnr2_auth_asym_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
_struct_ref_seq_dif.details
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_2
B
BGC
8
n
C
BGC
1
B
RER
9
n
C
RER
2
DGlcpb
b-D-glucopyranose
b-D-Glcp
Glc
Structure of bacteriophage T4 lysozyme refined at 1.7A resolution
RCSB
Y
RCSB
2011-05-05
REL
REL
oligosaccharide
WURCS=2.0/2,2,1/[a2122h-1b_1-5][ad621m-1a_1-5_3*C_3*N]/1-2/a2-b1
3
PDB2Glycan
1.1.0
WURCS
[][D-1-deoxy-Glcp]{[(2+1)][a-L-2-deoxy-Fucp3N]{}}
3
PDB-CARE
LINUCS
C1
O2
RER
BGC
2
1
3
O1
HO2
sing
n
n
MPD
(4S)-2-METHYL-2,4-PENTANEDIOL
MRD
(4R)-2-METHYLPENTANE-2,4-DIOL
PO4
PHOSPHATE ION
TRS
2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
CL
CHLORIDE ION
IPA
ISOPROPYL ALCOHOL
HOH
water
VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS
A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS
FURTHER GLYCOSYLATED BY A DISACCHARIDE MADE OF D-GLUCOSE
AND VANCOSAMINE.
HERE, VANCOMYCIN IS REPRESENTED BY GROUPING TOGETHER THE
SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER.
GROUP: 1
NAME: VANCOMYCIN
CHAIN: B
COMPONENT_1: PEPTIDE LIKE SEQUENCE RESIDUES 1 TO 7
COMPONENT_2: SUGAR (2-MER) RESIDUES 8 AND 9
DESCRIPTION: VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE,
GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8
AND 9) ON RESIDUE 4.
VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE. THE SCAFFOLD IS
A HEPTAPEPTIDE WITH THE CONFIGURATION D-D-L-D-D-L-L. IT IS
FURTHER GLYCOSYLATED BY A DISACCHARIDE MADE OF D-GLUCOSE
AND VANCOSAMINE.
HERE, VANCOMYCIN IS REPRESENTED BY GROUPING TOUGHER THE
SEQUENCE (SEQRES) AND THE TWO LIGANDS (HET) BGC AND RER.
THE AUTHORS STATE THAT THESE RESIDUES ARE LIGATED NON-RECOMBINANTLY WITH NATIVE PROTEIN LIGATION AFTER PROTEIN EXPRESSION AND PURIFICATION.
2LZM
PDB
experimental model
Antibiotic
VANCOMYCIN IS A TRICYCLIC GLYCOPEPTIDE,
GLYCOSYLATED BY A DISACCHARIDE (RESIDUES 8
AND 9) ON RESIDUE 4.
VANCOMYCIN
Glycopeptide
MPD
201
4
MPD
MPD
201
A
MRD
202
5
MRD
MRD
202
A
PO4
203
6
PO4
PO4
203
A
TRS
204
7
TRS
TRS
204
A
CL
205
8
CL
CL
205
A
IPA
206
9
IPA
IPA
206
A
IPA
207
9
IPA
IPA
207
A
MRD
103
5
MRD
MRD
103
B
HOH
301
10
HOH
HOH
301
A
HOH
302
10
HOH
HOH
302
A
HOH
303
10
HOH
HOH
303
A
HOH
304
10
HOH
HOH
304
A
HOH
305
10
HOH
HOH
305
A
HOH
306
10
HOH
HOH
306
A
HOH
307
10
HOH
HOH
307
A
HOH
308
10
HOH
HOH
308
A
HOH
309
10
HOH
HOH
309
A
HOH
310
10
HOH
HOH
310
A
HOH
311
10
HOH
HOH
311
A
HOH
312
10
HOH
HOH
312
A
HOH
313
10
HOH
HOH
313
A
HOH
314
10
HOH
HOH
314
A
HOH
315
10
HOH
HOH
315
A
HOH
316
10
HOH
HOH
316
A
HOH
317
10
HOH
HOH
317
A
HOH
318
10
HOH
HOH
318
A
HOH
319
10
HOH
HOH
319
A
HOH
320
10
HOH
HOH
320
A
HOH
321
10
HOH
HOH
321
A
HOH
322
10
HOH
HOH
322
A
HOH
323
10
HOH
HOH
323
A
HOH
324
10
HOH
HOH
324
A
HOH
325
10
HOH
HOH
325
A
HOH
326
10
HOH
HOH
326
A
HOH
327
10
HOH
HOH
327
A
HOH
328
10
HOH
HOH
328
A
HOH
329
10
HOH
HOH
329
A
HOH
330
10
HOH
HOH
330
A
HOH
331
10
HOH
HOH
331
A
HOH
332
10
HOH
HOH
332
A
HOH
333
10
HOH
HOH
333
A
HOH
334
10
HOH
HOH
334
A
HOH
335
10
HOH
HOH
335
A
HOH
336
10
HOH
HOH
336
A
HOH
337
10
HOH
HOH
337
A
HOH
338
10
HOH
HOH
338
A
HOH
339
10
HOH
HOH
339
A
HOH
340
10
HOH
HOH
340
A
HOH
341
10
HOH
HOH
341
A
HOH
342
10
HOH
HOH
342
A
HOH
343
10
HOH
HOH
343
A
HOH
344
10
HOH
HOH
344
A
HOH
345
10
HOH
HOH
345
A
HOH
346
10
HOH
HOH
346
A
HOH
347
10
HOH
HOH
347
A
HOH
348
10
HOH
HOH
348
A
HOH
349
10
HOH
HOH
349
A
HOH
350
10
HOH
HOH
350
A
HOH
351
10
HOH
HOH
351
A
HOH
352
10
HOH
HOH
352
A
HOH
353
10
HOH
HOH
353
A
HOH
354
10
HOH
HOH
354
A
HOH
355
10
HOH
HOH
355
A
HOH
356
10
HOH
HOH
356
A
HOH
357
10
HOH
HOH
357
A
HOH
358
10
HOH
HOH
358
A
HOH
359
10
HOH
HOH
359
A
HOH
360
10
HOH
HOH
360
A
HOH
361
10
HOH
HOH
361
A
HOH
362
10
HOH
HOH
362
A
HOH
363
10
HOH
HOH
363
A
HOH
364
10
HOH
HOH
364
A
HOH
365
10
HOH
HOH
365
A
HOH
366
10
HOH
HOH
366
A
HOH
367
10
HOH
HOH
367
A
HOH
368
10
HOH
HOH
368
A
HOH
369
10
HOH
HOH
369
A
HOH
370
10
HOH
HOH
370
A
HOH
371
10
HOH
HOH
371
A
HOH
372
10
HOH
HOH
372
A
HOH
373
10
HOH
HOH
373
A
HOH
374
10
HOH
HOH
374
A
HOH
375
10
HOH
HOH
375
A
HOH
376
10
HOH
HOH
376
A
HOH
377
10
HOH
HOH
377
A
HOH
378
10
HOH
HOH
378
A
HOH
379
10
HOH
HOH
379
A
HOH
380
10
HOH
HOH
380
A
HOH
381
10
HOH
HOH
381
A
HOH
382
10
HOH
HOH
382
A
HOH
383
10
HOH
HOH
383
A
HOH
384
10
HOH
HOH
384
A
HOH
385
10
HOH
HOH
385
A
HOH
386
10
HOH
HOH
386
A
HOH
387
10
HOH
HOH
387
A
HOH
388
10
HOH
HOH
388
A
HOH
389
10
HOH
HOH
389
A
HOH
390
10
HOH
HOH
390
A
HOH
391
10
HOH
HOH
391
A
HOH
392
10
HOH
HOH
392
A
HOH
393
10
HOH
HOH
393
A
HOH
394
10
HOH
HOH
394
A
HOH
395
10
HOH
HOH
395
A
HOH
396
10
HOH
HOH
396
A
HOH
397
10
HOH
HOH
397
A
HOH
398
10
HOH
HOH
398
A
HOH
399
10
HOH
HOH
399
A
HOH
400
10
HOH
HOH
400
A
HOH
401
10
HOH
HOH
401
A
HOH
402
10
HOH
HOH
402
A
HOH
403
10
HOH
HOH
403
A
HOH
404
10
HOH
HOH
404
A
HOH
405
10
HOH
HOH
405
A
HOH
406
10
HOH
HOH
406
A
HOH
407
10
HOH
HOH
407
A
HOH
408
10
HOH
HOH
408
A
HOH
409
10
HOH
HOH
409
A
HOH
410
10
HOH
HOH
410
A
HOH
411
10
HOH
HOH
411
A
HOH
412
10
HOH
HOH
412
A
HOH
413
10
HOH
HOH
413
A
HOH
414
10
HOH
HOH
414
A
HOH
415
10
HOH
HOH
415
A
HOH
416
10
HOH
HOH
416
A
HOH
417
10
HOH
HOH
417
A
HOH
418
10
HOH
HOH
418
A
HOH
419
10
HOH
HOH
419
A
HOH
420
10
HOH
HOH
420
A
HOH
421
10
HOH
HOH
421
A
HOH
422
10
HOH
HOH
422
A
HOH
423
10
HOH
HOH
423
A
HOH
424
10
HOH
HOH
424
A
HOH
425
10
HOH
HOH
425
A
HOH
426
10
HOH
HOH
426
A
HOH
427
10
HOH
HOH
427
A
HOH
428
10
HOH
HOH
428
A
HOH
429
10
HOH
HOH
429
A
HOH
430
10
HOH
HOH
430
A
HOH
431
10
HOH
HOH
431
A
HOH
432
10
HOH
HOH
432
A
HOH
433
10
HOH
HOH
433
A
HOH
434
10
HOH
HOH
434
A
HOH
435
10
HOH
HOH
435
A
HOH
436
10
HOH
HOH
436
A
HOH
437
10
HOH
HOH
437
A
HOH
438
10
HOH
HOH
438
A
HOH
439
10
HOH
HOH
439
A
HOH
440
10
HOH
HOH
440
A
HOH
441
10
HOH
HOH
441
A
HOH
442
10
HOH
HOH
442
A
HOH
443
10
HOH
HOH
443
A
HOH
444
10
HOH
HOH
444
A
HOH
445
10
HOH
HOH
445
A
HOH
446
10
HOH
HOH
446
A
HOH
447
10
HOH
HOH
447
A
HOH
448
10
HOH
HOH
448
A
HOH
449
10
HOH
HOH
449
A
HOH
450
10
HOH
HOH
450
A
HOH
451
10
HOH
HOH
451
A
HOH
452
10
HOH
HOH
452
A
HOH
453
10
HOH
HOH
453
A
HOH
454
10
HOH
HOH
454
A
HOH
455
10
HOH
HOH
455
A
HOH
456
10
HOH
HOH
456
A
HOH
457
10
HOH
HOH
457
A
HOH
458
10
HOH
HOH
458
A
HOH
459
10
HOH
HOH
459
A
HOH
460
10
HOH
HOH
460
A
HOH
461
10
HOH
HOH
461
A
HOH
462
10
HOH
HOH
462
A
HOH
463
10
HOH
HOH
463
A
HOH
464
10
HOH
HOH
464
A
HOH
465
10
HOH
HOH
465
A
HOH
466
10
HOH
HOH
466
A
HOH
467
10
HOH
HOH
467
A
HOH
468
10
HOH
HOH
468
A
HOH
469
10
HOH
HOH
469
A
HOH
470
10
HOH
HOH
470
A
HOH
471
10
HOH
HOH
471
A
HOH
472
10
HOH
HOH
472
A
HOH
473
10
HOH
HOH
473
A
HOH
474
10
HOH
HOH
474
A
HOH
475
10
HOH
HOH
475
A
HOH
476
10
HOH
HOH
476
A
HOH
477
10
HOH
HOH
477
A
HOH
478
10
HOH
HOH
478
A
HOH
479
10
HOH
HOH
479
A
HOH
480
10
HOH
HOH
480
A
HOH
481
10
HOH
HOH
481
A
HOH
482
10
HOH
HOH
482
A
HOH
483
10
HOH
HOH
483
A
HOH
484
10
HOH
HOH
484
A
HOH
485
10
HOH
HOH
485
A
HOH
486
10
HOH
HOH
486
A
HOH
487
10
HOH
HOH
487
A
HOH
488
10
HOH
HOH
488
A
HOH
489
10
HOH
HOH
489
A
HOH
490
10
HOH
HOH
490
A
HOH
491
10
HOH
HOH
491
A
HOH
492
10
HOH
HOH
492
A
HOH
493
10
HOH
HOH
493
A
HOH
494
10
HOH
HOH
494
A
HOH
495
10
HOH
HOH
495
A
HOH
496
10
HOH
HOH
496
A
HOH
497
10
HOH
HOH
497
A
HOH
498
10
HOH
HOH
498
A
HOH
499
10
HOH
HOH
499
A
HOH
500
10
HOH
HOH
500
A
HOH
501
10
HOH
HOH
501
A
HOH
502
10
HOH
HOH
502
A
HOH
503
10
HOH
HOH
503
A
HOH
504
10
HOH
HOH
504
A
HOH
505
10
HOH
HOH
505
A
HOH
506
10
HOH
HOH
506
A
HOH
507
10
HOH
HOH
507
A
HOH
508
10
HOH
HOH
508
A
HOH
509
10
HOH
HOH
509
A
HOH
510
10
HOH
HOH
510
A
HOH
511
10
HOH
HOH
511
A
HOH
512
10
HOH
HOH
512
A
HOH
513
10
HOH
HOH
513
A
HOH
514
10
HOH
HOH
514
A
HOH
515
10
HOH
HOH
515
A
HOH
516
10
HOH
HOH
516
A
HOH
517
10
HOH
HOH
517
A
HOH
518
10
HOH
HOH
518
A
HOH
519
10
HOH
HOH
519
A
HOH
520
10
HOH
HOH
520
A
HOH
521
10
HOH
HOH
521
A
HOH
522
10
HOH
HOH
522
A
HOH
523
10
HOH
HOH
523
A
HOH
524
10
HOH
HOH
524
A
HOH
525
10
HOH
HOH
525
A
HOH
526
10
HOH
HOH
526
A
HOH
527
10
HOH
HOH
527
A
HOH
528
10
HOH
HOH
528
A
HOH
529
10
HOH
HOH
529
A
HOH
530
10
HOH
HOH
530
A
HOH
531
10
HOH
HOH
531
A
HOH
532
10
HOH
HOH
532
A
HOH
533
10
HOH
HOH
533
A
HOH
534
10
HOH
HOH
534
A
HOH
535
10
HOH
HOH
535
A
HOH
536
10
HOH
HOH
536
A
HOH
537
10
HOH
HOH
537
A
HOH
538
10
HOH
HOH
538
A
HOH
539
10
HOH
HOH
539
A
HOH
540
10
HOH
HOH
540
A
HOH
541
10
HOH
HOH
541
A
HOH
542
10
HOH
HOH
542
A
HOH
543
10
HOH
HOH
543
A
HOH
544
10
HOH
HOH
544
A
HOH
545
10
HOH
HOH
545
A
HOH
546
10
HOH
HOH
546
A
HOH
547
10
HOH
HOH
547
A
HOH
548
10
HOH
HOH
548
A
HOH
549
10
HOH
HOH
549
A
HOH
550
10
HOH
HOH
550
A
HOH
551
10
HOH
HOH
551
A
HOH
552
10
HOH
HOH
552
A
HOH
553
10
HOH
HOH
553
A
HOH
554
10
HOH
HOH
554
A
HOH
555
10
HOH
HOH
555
A
HOH
556
10
HOH
HOH
556
A
HOH
557
10
HOH
HOH
557
A
HOH
558
10
HOH
HOH
558
A
HOH
559
10
HOH
HOH
559
A
HOH
560
10
HOH
HOH
560
A
HOH
561
10
HOH
HOH
561
A
HOH
562
10
HOH
HOH
562
A
HOH
563
10
HOH
HOH
563
A
HOH
564
10
HOH
HOH
564
A
HOH
565
10
HOH
HOH
565
A
HOH
566
10
HOH
HOH
566
A
HOH
567
10
HOH
HOH
567
A
HOH
568
10
HOH
HOH
568
A
HOH
569
10
HOH
HOH
569
A
HOH
570
10
HOH
HOH
570
A
HOH
571
10
HOH
HOH
571
A
HOH
572
10
HOH
HOH
572
A
HOH
573
10
HOH
HOH
573
A
HOH
574
10
HOH
HOH
574
A
HOH
575
10
HOH
HOH
575
A
HOH
576
10
HOH
HOH
576
A
HOH
577
10
HOH
HOH
577
A
HOH
578
10
HOH
HOH
578
A
HOH
579
10
HOH
HOH
579
A
HOH
580
10
HOH
HOH
580
A
HOH
581
10
HOH
HOH
581
A
HOH
582
10
HOH
HOH
582
A
HOH
583
10
HOH
HOH
583
A
HOH
584
10
HOH
HOH
584
A
HOH
585
10
HOH
HOH
585
A
HOH
586
10
HOH
HOH
586
A
HOH
587
10
HOH
HOH
587
A
HOH
588
10
HOH
HOH
588
A
HOH
589
10
HOH
HOH
589
A
HOH
590
10
HOH
HOH
590
A
HOH
591
10
HOH
HOH
591
A
HOH
592
10
HOH
HOH
592
A
HOH
593
10
HOH
HOH
593
A
HOH
594
10
HOH
HOH
594
A
HOH
595
10
HOH
HOH
595
A
HOH
596
10
HOH
HOH
596
A
HOH
597
10
HOH
HOH
597
A
HOH
598
10
HOH
HOH
598
A
HOH
599
10
HOH
HOH
599
A
HOH
600
10
HOH
HOH
600
A
HOH
601
10
HOH
HOH
601
A
HOH
602
10
HOH
HOH
602
A
HOH
603
10
HOH
HOH
603
A
HOH
201
10
HOH
HOH
201
B
HOH
202
10
HOH
HOH
202
B
HOH
203
10
HOH
HOH
203
B
HOH
204
10
HOH
HOH
204
B
HOH
205
10
HOH
HOH
205
B
HOH
206
10
HOH
HOH
206
B
HOH
207
10
HOH
HOH
207
B
HOH
208
10
HOH
HOH
208
B
HOH
209
10
HOH
HOH
209
B
HOH
210
10
HOH
HOH
210
B
HOH
211
10
HOH
HOH
211
B
HOH
212
10
HOH
HOH
212
B
HOH
213
10
HOH
HOH
213
B
1.560
1.560
19.780
19.780
MET
1
n
1
MET
1
A
ASN
2
n
2
ASN
2
A
ILE
3
n
3
ILE
3
A
PHE
4
n
4
PHE
4
A
GLU
5
n
5
GLU
5
A
MET
6
n
6
MET
6
A
LEU
7
n
7
LEU
7
A
ARG
8
n
8
ARG
8
A
ILE
9
n
9
ILE
9
A
ASP
10
n
10
ASP
10
A
GLU
11
n
11
GLU
11
A
GLY
12
n
12
GLY
12
A
LEU
13
n
13
LEU
13
A
ARG
14
n
14
ARG
14
A
LEU
15
n
15
LEU
15
A
LYS
16
n
16
LYS
16
A
ILE
17
n
17
ILE
17
A
TYR
18
n
18
TYR
18
A
LYS
19
n
19
LYS
19
A
ASP
20
n
20
ASP
20
A
THR
21
n
21
THR
21
A
GLU
22
n
22
GLU
22
A
GLY
23
n
23
GLY
23
A
TYR
24
n
24
TYR
24
A
TYR
25
n
25
TYR
25
A
THR
26
n
26
THR
26
A
ILE
27
n
27
ILE
27
A
GLY
28
n
28
GLY
28
A
ILE
29
n
29
ILE
29
A
GLY
30
n
30
GLY
30
A
HIS
31
n
31
HIS
31
A
LEU
32
n
32
LEU
32
A
LEU
33
n
33
LEU
33
A
THR
34
n
34
THR
34
A
LYS
35
n
35
LYS
35
A
SER
36
n
36
SER
36
A
PRO
37
n
37
PRO
37
A
SER
38
n
38
SER
38
A
LEU
39
n
39
LEU
39
A
ASN
40
n
40
ASN
40
A
ALA
41
n
41
ALA
41
A
ALA
42
n
42
ALA
42
A
LYS
43
n
43
LYS
43
A
SER
44
n
44
SER
44
A
GLU
45
n
45
GLU
45
A
LEU
46
n
46
LEU
46
A
ASP
47
n
47
ASP
47
A
LYS
48
n
48
LYS
48
A
ALA
49
n
49
ALA
49
A
ILE
50
n
50
ILE
50
A
GLY
51
n
51
GLY
51
A
ARG
52
n
52
ARG
52
A
ASN
53
n
53
ASN
53
A
THR
54
n
54
THR
54
A
ASN
55
n
55
ASN
55
A
GLY
56
n
56
GLY
56
A
VAL
57
n
57
VAL
57
A
ILE
58
n
58
ILE
58
A
THR
59
n
59
THR
59
A
LYS
60
n
60
LYS
60
A
ASP
61
n
61
ASP
61
A
GLU
62
n
62
GLU
62
A
ALA
63
n
63
ALA
63
A
GLU
64
n
64
GLU
64
A
LYS
65
n
65
LYS
65
A
LEU
66
n
66
LEU
66
A
PHE
67
n
67
PHE
67
A
ASN
68
n
68
ASN
68
A
GLN
69
n
69
GLN
69
A
ASP
70
n
70
ASP
70
A
VAL
71
n
71
VAL
71
A
ASP
72
n
72
ASP
72
A
ALA
73
n
73
ALA
73
A
ALA
74
n
74
ALA
74
A
VAL
75
n
75
VAL
75
A
ARG
76
n
76
ARG
76
A
GLY
77
n
77
GLY
77
A
ILE
78
n
78
ILE
78
A
LEU
79
n
79
LEU
79
A
ARG
80
n
80
ARG
80
A
ASN
81
n
81
ASN
81
A
ALA
82
n
82
ALA
82
A
LYS
83
n
83
LYS
83
A
LEU
84
n
84
LEU
84
A
LYS
85
n
85
LYS
85
A
PRO
86
n
86
PRO
86
A
VAL
87
n
87
VAL
87
A
TYR
88
n
88
TYR
88
A
ASP
89
n
89
ASP
89
A
SER
90
n
90
SER
90
A
LEU
91
n
91
LEU
91
A
ASP
92
n
92
ASP
92
A
ALA
93
n
93
ALA
93
A
VAL
94
n
94
VAL
94
A
ARG
95
n
95
ARG
95
A
ARG
96
n
96
ARG
96
A
ALA
97
n
97
ALA
97
A
ALA
98
n
98
ALA
98
A
LEU
99
n
99
LEU
99
A
ILE
100
n
100
ILE
100
A
ASN
101
n
101
ASN
101
A
MET
102
n
102
MET
102
A
VAL
103
n
103
VAL
103
A
PHE
104
n
104
PHE
104
A
GLN
105
n
105
GLN
105
A
MET
106
n
106
MET
106
A
GLY
107
n
107
GLY
107
A
GLU
108
n
108
GLU
108
A
THR
109
n
109
THR
109
A
GLY
110
n
110
GLY
110
A
VAL
111
n
111
VAL
111
A
ALA
112
n
112
ALA
112
A
GLY
113
n
113
GLY
113
A
PHE
114
n
114
PHE
114
A
THR
115
n
115
THR
115
A
ASN
116
n
116
ASN
116
A
SER
117
n
117
SER
117
A
LEU
118
n
118
LEU
118
A
ARG
119
n
119
ARG
119
A
MET
120
n
120
MET
120
A
LEU
121
n
121
LEU
121
A
GLN
122
n
122
GLN
122
A
GLN
123
n
123
GLN
123
A
LYS
124
n
124
LYS
124
A
ARG
125
n
125
ARG
125
A
TRP
126
n
126
TRP
126
A
ASP
127
n
127
ASP
127
A
GLU
128
n
128
GLU
128
A
ALA
129
n
129
ALA
129
A
ALA
130
n
130
ALA
130
A
VAL
131
n
131
VAL
131
A
ASN
132
n
132
ASN
132
A
LEU
133
n
133
LEU
133
A
ALA
134
n
134
ALA
134
A
LYS
135
n
135
LYS
135
A
SER
136
n
136
SER
136
A
ARG
137
n
137
ARG
137
A
TRP
138
n
138
TRP
138
A
TYR
139
n
139
TYR
139
A
ASN
140
n
140
ASN
140
A
GLN
141
n
141
GLN
141
A
THR
142
n
142
THR
142
A
PRO
143
n
143
PRO
143
A
ASN
144
n
144
ASN
144
A
ARG
145
n
145
ARG
145
A
ALA
146
n
146
ALA
146
A
LYS
147
n
147
LYS
147
A
ARG
148
n
148
ARG
148
A
VAL
149
n
149
VAL
149
A
ILE
150
n
150
ILE
150
A
THR
151
n
151
THR
151
A
THR
152
n
152
THR
152
A
PHE
153
n
153
PHE
153
A
ARG
154
n
154
ARG
154
A
THR
155
n
155
THR
155
A
GLY
156
n
156
GLY
156
A
THR
157
n
157
THR
157
A
TRP
158
n
158
TRP
158
A
ASP
159
n
159
ASP
159
A
ALA
160
n
160
ALA
160
A
TYR
161
n
161
TYR
161
A
LYS
162
n
162
LYS
162
A
ASN
163
n
163
ASN
163
A
ALA
164
n
164
ALA
164
A
CCS
165
n
165
CCS
165
A
LYS
166
n
166
LYS
166
A
DAL
167
n
167
DAL
167
A
DAL
168
n
168
DAL
168
A
MLU
1
n
1
MLU
1
B
OMZ
2
n
2
OMZ
2
B
ASN
3
n
3
ASN
3
B
GHP
4
n
4
GHP
4
B
GHP
5
n
5
GHP
5
B
OMY
6
n
6
OMY
6
B
3FG
7
n
7
3FG
7
B
author_defined_assembly
2
dimeric
A
CCS
165
CARBOXYMETHYLATED CYSTEINE
A
CCS
165
CYS
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
TYR
18
A
N
TYR
18
A
O
THR
26
A
O
THR
26
A
N
TYR
25
A
N
TYR
25
A
O
LEU
33
A
O
LEU
33
1
A
HOH
535
L
HOH
1
B
HOH
206
M
HOH
64.450
5.330
-0.3277
-0.0000
0.0000
-0.3277
-0.0000
0.6554
0.1799
0.1475
0.1491
1.4000
19.7840
3879
77081
5.0300
98.8800
1.000
0.300
0.9234
0.1800
RANDOM
1
1.430
MOLECULAR REPLACEMENT
14.5000
0.3800
0.7000
2LZM
ML
FLAT BULK SOLVENT MODEL
54.717
0.394
1.4000
19.7840
316
1798
67
0
1415
0.008
1541
1.317
2099
15.028
599
0.069
234
0.007
257
0.2684
0.2370
1.4501
377
6604
10
89.00
0.2008
0.1834
1.5081
369
7389
10
99.00
0.1918
0.1658
1.5768
407
7359
10
100.00
0.1954
0.1447
1.6598
403
7421
10
100.00
0.1745
0.1309
1.7638
421
7366
10
100.00
0.1576
0.1203
1.8999
368
7424
10
100.00
0.1715
0.1397
2.0909
403
7383
10
100.00
0.1709
0.1374
2.3930
378
7406
10
100.00
0.1804
0.1452
3.0132
391
7416
10
100.00
0.1730
0.1490
19.7856
362
7434
10
100.00
18.614
1.400
19.8
3RUN
77978
77081
-3.000
0.076
1
13.750
5.48
98.800
0.767
0.652
1.400
1.440
2.040
19858
5816
5100
0.745
1
87.700
0.565
0.533
1.440
1.480
2.900
25898
5616
5464
0.597
1
97.300
0.425
0.456
1.480
1.520
3.820
30478
5491
5491
0.504
1
100.000
0.335
0.357
1.520
1.570
4.810
29463
5286
5286
0.394
1
100.000
0.280
0.304
1.570
1.620
5.610
28566
5108
5107
0.336
1
100.000
0.237
0.256
1.620
1.670
6.530
28005
4991
4991
0.282
1
100.000
0.181
0.209
1.670
1.740
7.940
27119
4812
4812
0.230
1
100.000
0.152
0.174
1.740
1.810
9.350
26186
4633
4632
0.192
1
100.000
0.118
0.137
1.810
1.890
11.530
25186
4435
4434
0.151
1
100.000
0.093
0.109
1.890
1.980
13.930
23855
4200
4200
0.120
1
100.000
0.067
0.085
1.980
2.090
17.620
23103
4052
4051
0.094
1
100.000
0.051
0.070
2.090
2.210
20.760
21687
3789
3789
0.077
1
100.000
0.042
0.061
2.210
2.370
23.270
20628
3602
3602
0.067
1
100.000
0.038
0.057
2.370
2.560
24.440
19098
3333
3333
0.063
1
100.000
0.035
0.051
2.560
2.800
27.380
17592
3053
3053
0.056
1
100.000
0.029
0.046
2.800
3.130
30.460
15992
2775
2775
0.051
1
100.000
0.023
0.041
3.130
3.610
34.730
14074
2452
2452
0.045
1
100.000
0.021
0.041
3.610
4.430
37.400
11829
2066
2066
0.045
1
100.000
0.023
0.041
4.430
6.260
35.990
9135
1593
1593
0.045
1
100.000
0.023
0.042
6.260
37.380
4766
875
850
0.047
1
97.100
data scaling
Wolfgang Kabsch
http://www.mpimf-heidelberg.mpg.de/~kabsch/xds/html_doc/xscale_program.html
XSCALE
package
phasing
Alexei Vaguine
alexei@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/molrep.html
MOLREP
program
refinement
Paul D. Adams
PDAdams@lbl.gov
C++
http://www.phenix-online.org/
PHENIX
package
1.6.2_432
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
XDS
New strategy to analyze structures of glycopeptide antibiotic-target complexes
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
6
N
N
7
N
N
8
N
N
9
N
N
9
N
N
5
N
N
10
N
N
10
N
N
A
ASN
2
A
ASN
2
HELX_P
A
GLY
12
A
GLY
12
1
1
11
A
SER
38
A
SER
38
HELX_P
A
GLY
51
A
GLY
51
1
2
14
A
THR
59
A
THR
59
HELX_P
A
ASN
81
A
ASN
81
1
3
23
A
LYS
83
A
LYS
83
HELX_P
A
LEU
91
A
LEU
91
1
4
9
A
ASP
92
A
ASP
92
HELX_P
A
GLY
107
A
GLY
107
1
5
16
A
GLY
107
A
GLY
107
HELX_P
A
GLY
113
A
GLY
113
1
6
7
A
PHE
114
A
PHE
114
HELX_P
A
GLN
123
A
GLN
123
1
7
10
A
ARG
125
A
ARG
125
HELX_P
A
LYS
135
A
LYS
135
1
8
11
A
SER
136
A
SER
136
HELX_P
A
THR
142
A
THR
142
1
9
7
A
THR
142
A
THR
142
HELX_P
A
GLY
156
A
GLY
156
1
10
15
A
TRP
158
A
TRP
158
HELX_P
A
LYS
162
A
LYS
162
5
11
5
covale
1.333
both
A
ALA
164
A
C
ALA
164
1_555
A
CCS
165
A
N
CCS
165
1_555
covale
1.326
both
A
CCS
165
A
C
CCS
165
1_555
A
LYS
166
A
N
LYS
166
1_555
covale
1.328
both
A
LYS
166
A
C
LYS
166
1_555
A
DAL
167
A
N
DAL
167
1_555
covale
1.326
both
A
DAL
167
A
C
DAL
167
1_555
A
DAL
168
A
N
DAL
168
1_555
covale
1.335
both
B
MLU
1
B
C
MLU
1
1_555
B
OMZ
2
B
N
OMZ
2
1_555
covale
1.337
both
B
OMZ
2
B
C
OMZ
2
1_555
B
ASN
3
B
N
ASN
3
1_555
covale
1.400
none
B
OMZ
2
B
OH
OMZ
2
1_555
B
GHP
4
B
C5
GHP
4
1_555
covale
1.336
both
B
ASN
3
B
C
ASN
3
1_555
B
GHP
4
B
N
GHP
4
1_555
covale
1.331
both
B
GHP
4
B
C
GHP
4
1_555
B
GHP
5
B
N
GHP
5
1_555
covale
1.398
none
B
GHP
4
B
C3
GHP
4
1_555
B
OMY
6
B
OCZ
OMY
6
1_555
covale
1.434
one
A
B
GHP
4
B
O4
GHP
4
1_555
C
BGC
1
C
C1
BGC
1_555
covale
1.430
one
B
B
GHP
4
B
O4
GHP
4
1_555
C
BGC
1
C
C1
BGC
1_555
covale
1.332
both
B
GHP
5
B
C
GHP
5
1_555
B
OMY
6
B
N
OMY
6
1_555
covale
1.419
none
B
GHP
5
B
C5
GHP
5
1_555
B
3FG
7
B
CG2
3FG
7
1_555
covale
1.326
both
B
OMY
6
B
C
OMY
6
1_555
B
3FG
7
B
N
3FG
7
1_555
covale
1.429
both
A
A
C
BGC
1
C
O2
BGC
1_555
C
RER
2
C
C1
RER
1_555
covale
1.431
both
B
B
C
BGC
1
C
O2
BGC
1_555
C
RER
2
C
C1
RER
1_555
HYDROLASE/ANTIBIOTIC
antibiotic, glycopeptide, native protein ligation, fusion, carboxymethylation of cysteine, vancomycin, HYDROLASE-ANTIBIOTIC complex
B
GHP
5
B
GHP
5
1
B
OMY
6
B
OMY
6
5.99
LYS_BPT4
UNP
1
1
P00720
MNIFEMLRIDEGLRLKIYKDTEGYYTIGIGHLLTKSPSLNAAKSELDKAIGRNCNGVITKDEAEKLFNQDVDAAVRGILR
NAKLKPVYDSLDAVRRCALINMVFQMGETGVAGFTNSLRMLQQKRWDEAAVNLAKSRWYNQTPNRAKRVITTFRTGTWDA
YKNL
NOR00681
NOR
2
NOR00681
1
164
3RUN
1
164
P00720
A
1
1
164
1
7
3RUN
1
7
3RUN
B
2
1
7
1
CYS
engineered mutation
THR
54
3RUN
A
P00720
UNP
54
54
1
CYS
engineered mutation
ALA
97
3RUN
A
P00720
UNP
97
97
1
LEU
engineered mutation
ALA
164
3RUN
A
P00720
UNP
164
164
1
SEE REMARK 999
CCS
165
3RUN
A
P00720
UNP
165
1
SEE REMARK 999
LYS
166
3RUN
A
P00720
UNP
166
1
SEE REMARK 999
DAL
167
3RUN
A
P00720
UNP
167
1
SEE REMARK 999
DAL
168
3RUN
A
P00720
UNP
168
3
anti-parallel
anti-parallel
A
ARG
14
A
ARG
14
A
LYS
19
A
LYS
19
A
TYR
25
A
TYR
25
A
GLY
28
A
GLY
28
A
HIS
31
A
HIS
31
A
THR
34
A
THR
34
154
P 32 2 1