0.007360
0.000000
0.000000
0.000000
0.011515
0.000000
0.000000
0.000000
0.022232
0.00000
0.00000
0.00000
Speir, J.A.
Abdel-Motal, U.M.
Jondal, M.
Wilson, I.A.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
135.870
86.840
44.980
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
C6 H13 N O2 S
163.238
n
2-AMINO-4-ETHYL SULFANYL BUTYRIC ACID
L-peptide linking
C6 H12 O5
164.156
alpha-L-fucopyranose
alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose
L-saccharide, alpha linking
C6 H12 O6
180.156
beta-D-galactopyranose
beta-D-galactose; D-galactose; galactose
D-saccharide, beta linking
C6 H12 O6
180.156
alpha-D-galactopyranose
alpha-D-galactose; D-galactose; galactose; ALPHA D-GALACTOSE
D-saccharide, alpha 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
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
C
N
92
N
S
N
93
N
C
N
94
N
O
N
95
N
C
N
96
N
C
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
H
N
109
N
H
N
110
N
H
N
111
R
C
N
112
S
C
N
113
R
C
N
114
S
C
N
115
S
C
N
116
N
C
N
117
N
O
N
118
N
O
N
119
N
O
N
120
N
O
N
121
N
O
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
R
C
N
135
R
C
N
136
S
C
N
137
R
C
N
138
R
C
N
139
N
C
N
140
N
O
N
141
N
O
N
142
N
O
N
143
N
O
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
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
S
C
N
159
R
C
N
160
S
C
N
161
R
C
N
162
R
C
N
163
N
C
N
164
N
O
N
165
N
O
N
166
N
O
N
167
N
O
N
168
N
O
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
N
N
183
S
C
N
184
N
C
N
185
N
O
N
186
N
C
N
187
N
C
N
188
N
C
N
189
N
O
N
190
N
N
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
N
N
203
S
C
N
204
N
C
N
205
N
O
N
206
N
C
N
207
N
C
N
208
N
C
N
209
N
O
N
210
N
O
N
211
N
O
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
N
N
222
N
C
N
223
N
C
N
224
N
O
N
225
N
O
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
H
N
230
N
H
N
231
N
N
N
232
S
C
N
233
N
C
N
234
N
O
N
235
N
C
Y
236
N
C
Y
237
N
N
Y
238
N
C
Y
239
N
C
Y
240
N
N
N
241
N
O
N
242
N
H
N
243
N
H
N
244
N
H
N
245
N
H
N
246
N
H
N
247
N
H
N
248
N
H
N
249
N
H
N
250
N
H
N
251
N
H
N
252
N
O
N
253
N
H
N
254
N
H
N
255
N
N
N
256
S
C
N
257
N
C
N
258
N
O
N
259
S
C
N
260
N
C
N
261
N
C
N
262
N
C
N
263
N
O
N
264
N
H
N
265
N
H
N
266
N
H
N
267
N
H
N
268
N
H
N
269
N
H
N
270
N
H
N
271
N
H
N
272
N
H
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
N
N
278
S
C
N
279
N
C
N
280
N
O
N
281
N
C
N
282
N
C
N
283
N
C
N
284
N
C
N
285
N
O
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
H
N
295
N
H
N
296
N
H
N
297
N
H
N
298
N
H
N
299
N
N
N
300
S
C
N
301
N
C
N
302
N
O
N
303
N
C
N
304
N
C
N
305
N
C
N
306
N
C
N
307
N
N
N
308
N
O
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
H
N
319
N
H
N
320
N
H
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
N
N
325
S
C
N
326
N
C
N
327
N
O
N
328
N
C
N
329
N
C
N
330
N
S
N
331
N
C
N
332
N
O
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
H
N
344
R
C
N
345
R
C
N
346
R
C
N
347
S
C
N
348
R
C
N
349
N
C
N
350
N
C
N
351
N
C
N
352
N
N
N
353
N
O
N
354
N
O
N
355
N
O
N
356
N
O
N
357
N
O
N
358
N
O
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
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
N
N
375
S
C
N
376
N
C
N
377
N
O
N
378
N
C
Y
379
N
C
Y
380
N
C
Y
381
N
C
Y
382
N
C
Y
383
N
C
Y
384
N
C
N
385
N
O
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
H
N
392
N
H
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
N
N
398
S
C
N
399
N
C
N
400
N
O
N
401
N
C
N
402
N
C
N
403
N
C
N
404
N
O
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
N
N
415
S
C
N
416
N
C
N
417
N
O
N
418
N
C
N
419
N
O
N
420
N
O
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
N
N
429
S
C
N
430
N
C
N
431
N
O
N
432
R
C
N
433
N
O
N
434
N
C
N
435
N
O
N
436
N
H
N
437
N
H
N
438
N
H
N
439
N
H
N
440
N
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
N
N
446
S
C
N
447
N
C
N
448
N
O
N
449
N
C
Y
450
N
C
Y
451
N
C
Y
452
N
C
Y
453
N
N
Y
454
N
C
Y
455
N
C
Y
456
N
C
Y
457
N
C
Y
458
N
C
N
459
N
O
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
H
N
464
N
H
N
465
N
H
N
466
N
H
N
467
N
H
N
468
N
H
N
469
N
H
N
470
N
H
N
471
N
H
N
472
N
N
N
473
S
C
N
474
N
C
N
475
N
O
N
476
N
C
Y
477
N
C
Y
478
N
C
Y
479
N
C
Y
480
N
C
Y
481
N
C
Y
482
N
C
N
483
N
O
N
484
N
O
N
485
N
H
N
486
N
H
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
H
N
495
N
H
N
496
N
N
N
497
S
C
N
498
N
C
N
499
N
O
N
500
N
C
N
501
N
C
N
502
N
C
N
503
N
O
N
504
N
H
N
505
N
H
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
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
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
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
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
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
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
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
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
sing
N
179
N
sing
N
180
N
sing
N
181
N
sing
N
182
N
doub
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
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
sing
N
200
N
sing
N
201
N
doub
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
doub
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
doub
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
doub
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
Y
233
N
sing
Y
234
N
doub
Y
235
N
doub
N
236
N
sing
Y
237
N
sing
N
238
N
sing
Y
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
doub
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
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
doub
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
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
doub
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
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
doub
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
doub
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
doub
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
Y
371
N
doub
Y
372
N
sing
Y
373
N
sing
N
374
N
sing
Y
375
N
doub
N
376
N
sing
Y
377
N
doub
N
378
N
sing
Y
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
doub
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
doub
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
doub
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
sing
N
433
N
sing
N
434
N
sing
N
435
N
doub
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
Y
440
N
doub
Y
441
N
sing
Y
442
N
sing
N
443
N
sing
Y
444
N
doub
Y
445
N
sing
Y
446
N
sing
N
447
N
sing
Y
448
N
sing
Y
449
N
doub
N
450
N
sing
Y
451
N
doub
N
452
N
sing
Y
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
doub
N
464
N
sing
N
465
N
sing
N
466
N
sing
N
467
N
sing
Y
468
N
doub
Y
469
N
sing
Y
470
N
sing
N
471
N
sing
Y
472
N
doub
N
473
N
sing
Y
474
N
doub
N
475
N
sing
Y
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
sing
N
483
N
sing
N
484
N
sing
N
485
N
sing
N
486
N
sing
N
487
N
doub
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
US
Immunity
IUNIEH
2048
1074-7613
10
51
61
10.1016/S1074-7613(00)80006-0
10023770
Crystal structure of an MHC class I presented glycopeptide that generates carbohydrate-specific CTL.
1999
GW
Eur.J.Immunol.
EJIMAF
0794
0014-2980
26
544
Immunization with Glycosylated Kb-Binding Peptides Generates Carbohydrate- Specific, Unrestricted Cytotoxic T Cells
1996
10.2210/pdb1kbg/pdb
pdb_00001kbg
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
133
1
DOUBLE-FOCUSING MIRRORS
IMAGE PLATE
1996-02-01
MARRESEARCH
NI FILTER
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
SIEMENS
FORMS HETERODIMER WITH CHAIN L, AND THEN A TRIMOLECULAR COMPLEX WITH CHAIN P
31648.322
PROTEIN (MAJOR HISTOCOMPATIBILITY COMPLEX CLASS I ANTIGEN H-2KB)
PEPTIDE-BINDING DOMAIN
1
man
polymer
FORMS HETERODIMER WITH CHAIN H, AND THEN A TRIMOLECULAR COMPLEX WITH CHAIN P
11704.359
PROTEIN (BETA-2-MICROGLOBULIN)
MHC ASSOCIATED LIGHT CHAIN
1
nat
polymer
VSV-8 DERIVED GLYCOPEPTIDE THAT FORMS A TRIMOLECULAR COMPLEX WITH CHAINS H AND L.
973.172
PROTEIN (SYNTHETIC GLYCOPEPTIDE RGY8-6H-GAL2)
H-2KB-BOUND GLYCOPEPTIDE
1
syn
polymer
570.542
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
1
man
branched
342.297
alpha-D-galactopyranose-(1-4)-beta-D-galactopyranose
1
man
branched
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
1
man
non-polymer
18.015
water
108
nat
water
KB
B2M
no
no
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYWERETQKAKGNEQSFRVDLRT
LLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDGCDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYL
EGTCVEWLRRYLKNGNATLLRTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRW
GPHSLRYFVTAVSRPGLGEPRYMEVGYVDDTEFVRFDSDAENPRYEPRARWMEQEGPEYWERETQKAKGNEQSFRVDLRT
LLGYYNQSKGGSHTIQVISGCEVGSDGRLLRGYQQYAYDGCDYIALNEDLKTWTAADMAALITKHKWEQAGEAERLRAYL
EGTCVEWLRRYLKNGNATLLRTDSPKAHVTHHSRPEDKVTLRCWALGFYPADITLTWQLNGEELIQDMELVETRPAGDGT
FQKWASVVVPLGKEQYYTCHVYHQGLPEPLTLRW
H
polypeptide(L)
no
no
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYAC
RVKHDSMAEPKTVYWDRDM
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYAC
RVKHDSMAEPKTVYWDRDM
L
polypeptide(L)
no
yes
RGYVY(ESC)GL
RGYVYMGL
P
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
house mouse
Mus
BALB/B
fruit fly
Drosophila
sample
TRUNCATED AFTER RESIDUE 274
MOST NUCLEATED CELLS
CYTOPLASM, ER, CELL SURFACE
10090
Mus musculus
SECRETED
7227
Drosophila melanogaster
house mouse
TRUNCATED AFTER RESIDUE 99
Mus
sample
MOST NUCLEATED CELLS
CYTOPLASM, ER, CELL SURFACE
10090
Mus musculus
BALB/B
1
2.86
57
6.4
2.3M Na/K PHOSPHATE, 2% MPD, pH 6.4
atom_site
chem_comp
entity
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_nonpoly_scheme
pdbx_struct_assembly_gen
struct_asym
struct_conn
struct_site
struct_site_gen
chem_comp
database_2
struct_ref_seq_dif
chem_comp_atom
chem_comp_bond
pdbx_initial_refinement_model
chem_comp_atom
chem_comp_bond
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Derived calculations
Version format compliance
Atomic model
Data collection
Derived calculations
Structure summary
Database references
Structure summary
Data collection
Refinement description
Data collection
1
0
1999-02-09
1
1
2007-10-21
1
2
2011-07-13
2
0
2020-07-29
2
1
2021-11-03
2
2
2023-08-16
2
3
2023-11-15
_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_asym_id
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_entity_id
_atom_site.type_symbol
_chem_comp.name
_chem_comp.type
_pdbx_struct_assembly_gen.asym_id_list
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_role
_struct_conn.pdbx_value_order
_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
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_ref_seq_dif.details
_chem_comp_atom.atom_id
_chem_comp_bond.atom_id_2
NAG
100
n
A
NAG
1
NAG
101
n
A
NAG
2
FUC
102
n
A
FUC
3
P
HGG
6
n
B
GAL
1
P
HGG
6
n
B
GLA
2
LFucpa
a-L-fucopyranose
a-L-Fucp
Fuc
DGalpb
b-D-galactopyranose
b-D-Galp
Gal
DGalpa
a-D-galactopyranose
a-D-Galp
Gal
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
BNL
Y
RCSB
1998-08-28
REL
oligosaccharide
oligosaccharide
DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-
4
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/2,3,2/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-1-2/a4-b1_a6-c1
4
PDB2Glycan
1.1.0
WURCS
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}[(6+1)][a-L-Fucp]{}}}
4
PDB-CARE
LINUCS
DGalpa1-4DGalpb1-ROH
5
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/2,2,1/[a2112h-1b_1-5][a2112h-1a_1-5]/1-2/a4-b1
5
PDB2Glycan
1.1.0
WURCS
[][b-D-Galp]{[(4+1)][a-D-Galp]{}}
5
PDB-CARE
LINUCS
C1
O4
NAG
NAG
2
1
4
O1
HO4
sing
C1
O6
FUC
NAG
3
1
4
O1
HO6
sing
C1
O4
GLA
GAL
2
1
5
O1
HO4
sing
n
n
n
n
n
NAG
2-acetamido-2-deoxy-beta-D-glucopyranose
HOH
water
VSV NUCLEOPROTEIN RESIDUES 52-59 COMMONLY REFERRED TO AS VSV-8 FROM THE VESICULAR STOMATITIS VIRUS. RESIDUE 57 IS REPLACED BY A SYNTHETIC GLYCOSYLATED AMINO ACID.
sample
2VAA
PDB ENTRY 2VAA
PDB
experimental model
NAG
1
6
NAG
NAG
1001
H
HOH
1
7
HOH
HOH
1103
H
HOH
2
7
HOH
HOH
1104
H
HOH
4
7
HOH
HOH
1105
H
HOH
5
7
HOH
HOH
1106
H
HOH
7
7
HOH
HOH
1107
H
HOH
9
7
HOH
HOH
1108
H
HOH
10
7
HOH
HOH
1109
H
HOH
11
7
HOH
HOH
1110
H
HOH
12
7
HOH
HOH
1111
H
HOH
13
7
HOH
HOH
1112
H
HOH
14
7
HOH
HOH
1113
H
HOH
15
7
HOH
HOH
1114
H
HOH
16
7
HOH
HOH
1115
H
HOH
17
7
HOH
HOH
1116
H
HOH
18
7
HOH
HOH
1117
H
HOH
20
7
HOH
HOH
1118
H
HOH
21
7
HOH
HOH
1119
H
HOH
22
7
HOH
HOH
1120
H
HOH
23
7
HOH
HOH
1121
H
HOH
24
7
HOH
HOH
1122
H
HOH
25
7
HOH
HOH
1123
H
HOH
27
7
HOH
HOH
1124
H
HOH
28
7
HOH
HOH
1125
H
HOH
29
7
HOH
HOH
1126
H
HOH
30
7
HOH
HOH
1127
H
HOH
31
7
HOH
HOH
1128
H
HOH
33
7
HOH
HOH
1129
H
HOH
34
7
HOH
HOH
1130
H
HOH
35
7
HOH
HOH
1131
H
HOH
38
7
HOH
HOH
1132
H
HOH
39
7
HOH
HOH
1133
H
HOH
41
7
HOH
HOH
1134
H
HOH
42
7
HOH
HOH
1135
H
HOH
43
7
HOH
HOH
1136
H
HOH
44
7
HOH
HOH
1137
H
HOH
45
7
HOH
HOH
1138
H
HOH
47
7
HOH
HOH
1139
H
HOH
48
7
HOH
HOH
1140
H
HOH
50
7
HOH
HOH
1141
H
HOH
51
7
HOH
HOH
1142
H
HOH
53
7
HOH
HOH
1143
H
HOH
54
7
HOH
HOH
1144
H
HOH
55
7
HOH
HOH
1145
H
HOH
57
7
HOH
HOH
1146
H
HOH
59
7
HOH
HOH
1147
H
HOH
65
7
HOH
HOH
1148
H
HOH
66
7
HOH
HOH
1149
H
HOH
67
7
HOH
HOH
1150
H
HOH
68
7
HOH
HOH
1151
H
HOH
69
7
HOH
HOH
1152
H
HOH
70
7
HOH
HOH
1153
H
HOH
71
7
HOH
HOH
1154
H
HOH
72
7
HOH
HOH
1155
H
HOH
73
7
HOH
HOH
1156
H
HOH
74
7
HOH
HOH
1157
H
HOH
75
7
HOH
HOH
1158
H
HOH
76
7
HOH
HOH
1159
H
HOH
77
7
HOH
HOH
1160
H
HOH
78
7
HOH
HOH
1161
H
HOH
79
7
HOH
HOH
1162
H
HOH
80
7
HOH
HOH
1163
H
HOH
82
7
HOH
HOH
1164
H
HOH
83
7
HOH
HOH
1165
H
HOH
85
7
HOH
HOH
1166
H
HOH
86
7
HOH
HOH
1167
H
HOH
88
7
HOH
HOH
1168
H
HOH
89
7
HOH
HOH
1169
H
HOH
90
7
HOH
HOH
1170
H
HOH
91
7
HOH
HOH
1171
H
HOH
92
7
HOH
HOH
1172
H
HOH
93
7
HOH
HOH
1173
H
HOH
94
7
HOH
HOH
1174
H
HOH
96
7
HOH
HOH
1175
H
HOH
97
7
HOH
HOH
1176
H
HOH
100
7
HOH
HOH
1177
H
HOH
101
7
HOH
HOH
1178
H
HOH
103
7
HOH
HOH
1179
H
HOH
104
7
HOH
HOH
1180
H
HOH
105
7
HOH
HOH
1181
H
HOH
106
7
HOH
HOH
1182
H
HOH
108
7
HOH
HOH
1183
H
HOH
3
7
HOH
HOH
100
L
HOH
6
7
HOH
HOH
101
L
HOH
8
7
HOH
HOH
102
L
HOH
19
7
HOH
HOH
103
L
HOH
26
7
HOH
HOH
104
L
HOH
32
7
HOH
HOH
105
L
HOH
36
7
HOH
HOH
106
L
HOH
37
7
HOH
HOH
107
L
HOH
40
7
HOH
HOH
108
L
HOH
46
7
HOH
HOH
109
L
HOH
49
7
HOH
HOH
110
L
HOH
52
7
HOH
HOH
111
L
HOH
56
7
HOH
HOH
112
L
HOH
58
7
HOH
HOH
113
L
HOH
60
7
HOH
HOH
114
L
HOH
61
7
HOH
HOH
115
L
HOH
62
7
HOH
HOH
116
L
HOH
63
7
HOH
HOH
117
L
HOH
64
7
HOH
HOH
118
L
HOH
81
7
HOH
HOH
119
L
HOH
84
7
HOH
HOH
120
L
HOH
98
7
HOH
HOH
121
L
HOH
102
7
HOH
HOH
122
L
HOH
107
7
HOH
HOH
123
L
HOH
87
7
HOH
HOH
87
P
HOH
95
7
HOH
HOH
95
P
HOH
99
7
HOH
HOH
99
P
GLY
1
n
1
GLY
1
H
PRO
2
n
2
PRO
2
H
HIS
3
n
3
HIS
3
H
SER
4
n
4
SER
4
H
LEU
5
n
5
LEU
5
H
ARG
6
n
6
ARG
6
H
TYR
7
n
7
TYR
7
H
PHE
8
n
8
PHE
8
H
VAL
9
n
9
VAL
9
H
THR
10
n
10
THR
10
H
ALA
11
n
11
ALA
11
H
VAL
12
n
12
VAL
12
H
SER
13
n
13
SER
13
H
ARG
14
n
14
ARG
14
H
PRO
15
n
15
PRO
15
H
GLY
16
n
16
GLY
16
H
LEU
17
n
17
LEU
17
H
GLY
18
n
18
GLY
18
H
GLU
19
n
19
GLU
19
H
PRO
20
n
20
PRO
20
H
ARG
21
n
21
ARG
21
H
TYR
22
n
22
TYR
22
H
MET
23
n
23
MET
23
H
GLU
24
n
24
GLU
24
H
VAL
25
n
25
VAL
25
H
GLY
26
n
26
GLY
26
H
TYR
27
n
27
TYR
27
H
VAL
28
n
28
VAL
28
H
ASP
29
n
29
ASP
29
H
ASP
30
n
30
ASP
30
H
THR
31
n
31
THR
31
H
GLU
32
n
32
GLU
32
H
PHE
33
n
33
PHE
33
H
VAL
34
n
34
VAL
34
H
ARG
35
n
35
ARG
35
H
PHE
36
n
36
PHE
36
H
ASP
37
n
37
ASP
37
H
SER
38
n
38
SER
38
H
ASP
39
n
39
ASP
39
H
ALA
40
n
40
ALA
40
H
GLU
41
n
41
GLU
41
H
ASN
42
n
42
ASN
42
H
PRO
43
n
43
PRO
43
H
ARG
44
n
44
ARG
44
H
TYR
45
n
45
TYR
45
H
GLU
46
n
46
GLU
46
H
PRO
47
n
47
PRO
47
H
ARG
48
n
48
ARG
48
H
ALA
49
n
49
ALA
49
H
ARG
50
n
50
ARG
50
H
TRP
51
n
51
TRP
51
H
MET
52
n
52
MET
52
H
GLU
53
n
53
GLU
53
H
GLN
54
n
54
GLN
54
H
GLU
55
n
55
GLU
55
H
GLY
56
n
56
GLY
56
H
PRO
57
n
57
PRO
57
H
GLU
58
n
58
GLU
58
H
TYR
59
n
59
TYR
59
H
TRP
60
n
60
TRP
60
H
GLU
61
n
61
GLU
61
H
ARG
62
n
62
ARG
62
H
GLU
63
n
63
GLU
63
H
THR
64
n
64
THR
64
H
GLN
65
n
65
GLN
65
H
LYS
66
n
66
LYS
66
H
ALA
67
n
67
ALA
67
H
LYS
68
n
68
LYS
68
H
GLY
69
n
69
GLY
69
H
ASN
70
n
70
ASN
70
H
GLU
71
n
71
GLU
71
H
GLN
72
n
72
GLN
72
H
SER
73
n
73
SER
73
H
PHE
74
n
74
PHE
74
H
ARG
75
n
75
ARG
75
H
VAL
76
n
76
VAL
76
H
ASP
77
n
77
ASP
77
H
LEU
78
n
78
LEU
78
H
ARG
79
n
79
ARG
79
H
THR
80
n
80
THR
80
H
LEU
81
n
81
LEU
81
H
LEU
82
n
82
LEU
82
H
GLY
83
n
83
GLY
83
H
TYR
84
n
84
TYR
84
H
TYR
85
n
85
TYR
85
H
ASN
86
n
86
ASN
86
H
GLN
87
n
87
GLN
87
H
SER
88
n
88
SER
88
H
LYS
89
n
89
LYS
89
H
GLY
90
n
90
GLY
90
H
GLY
91
n
91
GLY
91
H
SER
92
n
92
SER
92
H
HIS
93
n
93
HIS
93
H
THR
94
n
94
THR
94
H
ILE
95
n
95
ILE
95
H
GLN
96
n
96
GLN
96
H
VAL
97
n
97
VAL
97
H
ILE
98
n
98
ILE
98
H
SER
99
n
99
SER
99
H
GLY
100
n
100
GLY
100
H
CYS
101
n
101
CYS
101
H
GLU
102
n
102
GLU
102
H
VAL
103
n
103
VAL
103
H
GLY
104
n
104
GLY
104
H
SER
105
n
105
SER
105
H
ASP
106
n
106
ASP
106
H
GLY
107
n
107
GLY
107
H
ARG
108
n
108
ARG
108
H
LEU
109
n
109
LEU
109
H
LEU
110
n
110
LEU
110
H
ARG
111
n
111
ARG
111
H
GLY
112
n
112
GLY
112
H
TYR
113
n
113
TYR
113
H
GLN
114
n
114
GLN
114
H
GLN
115
n
115
GLN
115
H
TYR
116
n
116
TYR
116
H
ALA
117
n
117
ALA
117
H
TYR
118
n
118
TYR
118
H
ASP
119
n
119
ASP
119
H
GLY
120
n
120
GLY
120
H
CYS
121
n
121
CYS
121
H
ASP
122
n
122
ASP
122
H
TYR
123
n
123
TYR
123
H
ILE
124
n
124
ILE
124
H
ALA
125
n
125
ALA
125
H
LEU
126
n
126
LEU
126
H
ASN
127
n
127
ASN
127
H
GLU
128
n
128
GLU
128
H
ASP
129
n
129
ASP
129
H
LEU
130
n
130
LEU
130
H
LYS
131
n
131
LYS
131
H
THR
132
n
132
THR
132
H
TRP
133
n
133
TRP
133
H
THR
134
n
134
THR
134
H
ALA
135
n
135
ALA
135
H
ALA
136
n
136
ALA
136
H
ASP
137
n
137
ASP
137
H
MET
138
n
138
MET
138
H
ALA
139
n
139
ALA
139
H
ALA
140
n
140
ALA
140
H
LEU
141
n
141
LEU
141
H
ILE
142
n
142
ILE
142
H
THR
143
n
143
THR
143
H
LYS
144
n
144
LYS
144
H
HIS
145
n
145
HIS
145
H
LYS
146
n
146
LYS
146
H
TRP
147
n
147
TRP
147
H
GLU
148
n
148
GLU
148
H
GLN
149
n
149
GLN
149
H
ALA
150
n
150
ALA
150
H
GLY
151
n
151
GLY
151
H
GLU
152
n
152
GLU
152
H
ALA
153
n
153
ALA
153
H
GLU
154
n
154
GLU
154
H
ARG
155
n
155
ARG
155
H
LEU
156
n
156
LEU
156
H
ARG
157
n
157
ARG
157
H
ALA
158
n
158
ALA
158
H
TYR
159
n
159
TYR
159
H
LEU
160
n
160
LEU
160
H
GLU
161
n
161
GLU
161
H
GLY
162
n
162
GLY
162
H
THR
163
n
163
THR
163
H
CYS
164
n
164
CYS
164
H
VAL
165
n
165
VAL
165
H
GLU
166
n
166
GLU
166
H
TRP
167
n
167
TRP
167
H
LEU
168
n
168
LEU
168
H
ARG
169
n
169
ARG
169
H
ARG
170
n
170
ARG
170
H
TYR
171
n
171
TYR
171
H
LEU
172
n
172
LEU
172
H
LYS
173
n
173
LYS
173
H
ASN
174
n
174
ASN
174
H
GLY
175
n
175
GLY
175
H
ASN
176
n
176
ASN
176
H
ALA
177
n
177
ALA
177
H
THR
178
n
178
THR
178
H
LEU
179
n
179
LEU
179
H
LEU
180
n
180
LEU
180
H
ARG
181
n
181
ARG
181
H
THR
182
n
182
THR
182
H
ASP
183
n
183
ASP
183
H
SER
184
n
184
SER
184
H
PRO
185
n
185
PRO
185
H
LYS
186
n
186
LYS
186
H
ALA
187
n
187
ALA
187
H
HIS
188
n
188
HIS
188
H
VAL
189
n
189
VAL
189
H
THR
190
n
190
THR
190
H
HIS
191
n
191
HIS
191
H
HIS
192
n
192
HIS
192
H
SER
193
n
193
SER
193
H
ARG
194
n
194
ARG
194
H
PRO
195
n
195
PRO
195
H
GLU
196
n
196
GLU
196
H
ASP
197
n
197
ASP
197
H
LYS
198
n
198
LYS
198
H
VAL
199
n
199
VAL
199
H
THR
200
n
200
THR
200
H
LEU
201
n
201
LEU
201
H
ARG
202
n
202
ARG
202
H
CYS
203
n
203
CYS
203
H
TRP
204
n
204
TRP
204
H
ALA
205
n
205
ALA
205
H
LEU
206
n
206
LEU
206
H
GLY
207
n
207
GLY
207
H
PHE
208
n
208
PHE
208
H
TYR
209
n
209
TYR
209
H
PRO
210
n
210
PRO
210
H
ALA
211
n
211
ALA
211
H
ASP
212
n
212
ASP
212
H
ILE
213
n
213
ILE
213
H
THR
214
n
214
THR
214
H
LEU
215
n
215
LEU
215
H
THR
216
n
216
THR
216
H
TRP
217
n
217
TRP
217
H
GLN
218
n
218
GLN
218
H
LEU
219
n
219
LEU
219
H
ASN
220
n
220
ASN
220
H
GLY
221
n
221
GLY
221
H
GLU
222
n
222
GLU
222
H
GLU
223
n
223
GLU
223
H
LEU
224
n
224
LEU
224
H
ILE
225
n
225
ILE
225
H
GLN
226
n
226
GLN
226
H
ASP
227
n
227
ASP
227
H
MET
228
n
228
MET
228
H
GLU
229
n
229
GLU
229
H
LEU
230
n
230
LEU
230
H
VAL
231
n
231
VAL
231
H
GLU
232
n
232
GLU
232
H
THR
233
n
233
THR
233
H
ARG
234
n
234
ARG
234
H
PRO
235
n
235
PRO
235
H
ALA
236
n
236
ALA
236
H
GLY
237
n
237
GLY
237
H
ASP
238
n
238
ASP
238
H
GLY
239
n
239
GLY
239
H
THR
240
n
240
THR
240
H
PHE
241
n
241
PHE
241
H
GLN
242
n
242
GLN
242
H
LYS
243
n
243
LYS
243
H
TRP
244
n
244
TRP
244
H
ALA
245
n
245
ALA
245
H
SER
246
n
246
SER
246
H
VAL
247
n
247
VAL
247
H
VAL
248
n
248
VAL
248
H
VAL
249
n
249
VAL
249
H
PRO
250
n
250
PRO
250
H
LEU
251
n
251
LEU
251
H
GLY
252
n
252
GLY
252
H
LYS
253
n
253
LYS
253
H
GLU
254
n
254
GLU
254
H
GLN
255
n
255
GLN
255
H
TYR
256
n
256
TYR
256
H
TYR
257
n
257
TYR
257
H
THR
258
n
258
THR
258
H
CYS
259
n
259
CYS
259
H
HIS
260
n
260
HIS
260
H
VAL
261
n
261
VAL
261
H
TYR
262
n
262
TYR
262
H
HIS
263
n
263
HIS
263
H
GLN
264
n
264
GLN
264
H
GLY
265
n
265
GLY
265
H
LEU
266
n
266
LEU
266
H
PRO
267
n
267
PRO
267
H
GLU
268
n
268
GLU
268
H
PRO
269
n
269
PRO
269
H
LEU
270
n
270
LEU
270
H
THR
271
n
271
THR
271
H
LEU
272
n
272
LEU
272
H
ARG
273
n
273
ARG
273
H
TRP
274
n
274
TRP
274
H
ILE
1
n
1
ILE
1
L
GLN
2
n
2
GLN
2
L
LYS
3
n
3
LYS
3
L
THR
4
n
4
THR
4
L
PRO
5
n
5
PRO
5
L
GLN
6
n
6
GLN
6
L
ILE
7
n
7
ILE
7
L
GLN
8
n
8
GLN
8
L
VAL
9
n
9
VAL
9
L
TYR
10
n
10
TYR
10
L
SER
11
n
11
SER
11
L
ARG
12
n
12
ARG
12
L
HIS
13
n
13
HIS
13
L
PRO
14
n
14
PRO
14
L
PRO
15
n
15
PRO
15
L
GLU
16
n
16
GLU
16
L
ASN
17
n
17
ASN
17
L
GLY
18
n
18
GLY
18
L
LYS
19
n
19
LYS
19
L
PRO
20
n
20
PRO
20
L
ASN
21
n
21
ASN
21
L
ILE
22
n
22
ILE
22
L
LEU
23
n
23
LEU
23
L
ASN
24
n
24
ASN
24
L
CYS
25
n
25
CYS
25
L
TYR
26
n
26
TYR
26
L
VAL
27
n
27
VAL
27
L
THR
28
n
28
THR
28
L
GLN
29
n
29
GLN
29
L
PHE
30
n
30
PHE
30
L
HIS
31
n
31
HIS
31
L
PRO
32
n
32
PRO
32
L
PRO
33
n
33
PRO
33
L
HIS
34
n
34
HIS
34
L
ILE
35
n
35
ILE
35
L
GLU
36
n
36
GLU
36
L
ILE
37
n
37
ILE
37
L
GLN
38
n
38
GLN
38
L
MET
39
n
39
MET
39
L
LEU
40
n
40
LEU
40
L
LYS
41
n
41
LYS
41
L
ASN
42
n
42
ASN
42
L
GLY
43
n
43
GLY
43
L
LYS
44
n
44
LYS
44
L
LYS
45
n
45
LYS
45
L
ILE
46
n
46
ILE
46
L
PRO
47
n
47
PRO
47
L
LYS
48
n
48
LYS
48
L
VAL
49
n
49
VAL
49
L
GLU
50
n
50
GLU
50
L
MET
51
n
51
MET
51
L
SER
52
n
52
SER
52
L
ASP
53
n
53
ASP
53
L
MET
54
n
54
MET
54
L
SER
55
n
55
SER
55
L
PHE
56
n
56
PHE
56
L
SER
57
n
57
SER
57
L
LYS
58
n
58
LYS
58
L
ASP
59
n
59
ASP
59
L
TRP
60
n
60
TRP
60
L
SER
61
n
61
SER
61
L
PHE
62
n
62
PHE
62
L
TYR
63
n
63
TYR
63
L
ILE
64
n
64
ILE
64
L
LEU
65
n
65
LEU
65
L
ALA
66
n
66
ALA
66
L
HIS
67
n
67
HIS
67
L
THR
68
n
68
THR
68
L
GLU
69
n
69
GLU
69
L
PHE
70
n
70
PHE
70
L
THR
71
n
71
THR
71
L
PRO
72
n
72
PRO
72
L
THR
73
n
73
THR
73
L
GLU
74
n
74
GLU
74
L
THR
75
n
75
THR
75
L
ASP
76
n
76
ASP
76
L
THR
77
n
77
THR
77
L
TYR
78
n
78
TYR
78
L
ALA
79
n
79
ALA
79
L
CYS
80
n
80
CYS
80
L
ARG
81
n
81
ARG
81
L
VAL
82
n
82
VAL
82
L
LYS
83
n
83
LYS
83
L
HIS
84
n
84
HIS
84
L
ASP
85
n
85
ASP
85
L
SER
86
n
86
SER
86
L
MET
87
n
87
MET
87
L
ALA
88
n
88
ALA
88
L
GLU
89
n
89
GLU
89
L
PRO
90
n
90
PRO
90
L
LYS
91
n
91
LYS
91
L
THR
92
n
92
THR
92
L
VAL
93
n
93
VAL
93
L
TYR
94
n
94
TYR
94
L
TRP
95
n
95
TRP
95
L
ASP
96
n
96
ASP
96
L
ARG
97
n
97
ARG
97
L
ASP
98
n
98
ASP
98
L
MET
99
n
99
MET
99
L
ARG
1
n
1
ARG
1
P
GLY
2
n
2
GLY
2
P
TYR
3
n
3
TYR
3
P
VAL
4
n
4
VAL
4
P
TYR
5
n
5
TYR
5
P
HGG
6
n
6
ESC
6
P
GLY
7
n
7
GLY
7
P
LEU
8
n
8
LEU
8
P
author_and_software_defined_assembly
PISA,PQS
3
trimeric
5810
-1
19210
H
ASN
86
GLYCOSYLATION SITE
A
ASN
86
ASN
H
ASN
176
GLYCOSYLATION SITE
A
ASN
176
ASN
P
ESC
6
2-AMINO-4-ETHYL SULFANYL BUTYRIC ACID
C
ESC
6
MET
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
H
O
GLU
46
A
O
GLU
46
H
N
ARG
35
A
N
ARG
35
H
O
THR
31
A
O
THR
31
H
N
VAL
28
A
N
VAL
28
H
O
ARG
21
A
O
ARG
21
H
N
VAL
12
A
N
VAL
12
H
O
HIS
3
A
O
HIS
3
H
N
VAL
103
A
N
VAL
103
H
O
GLN
96
A
O
GLN
96
H
N
ALA
117
A
N
ALA
117
H
O
ALA
125
A
O
ALA
125
H
N
THR
134
A
N
THR
134
H
O
LYS
186
A
O
LYS
186
H
N
LEU
206
A
N
LEU
206
H
O
VAL
199
A
O
VAL
199
H
N
VAL
249
A
N
VAL
249
H
O
SER
246
A
O
SER
246
H
N
GLU
229
A
N
GLU
229
H
O
THR
214
A
O
THR
214
H
N
TYR
262
A
N
TYR
262
H
O
CYS
259
A
O
CYS
259
H
N
LEU
272
A
N
LEU
272
L
O
GLN
6
B
O
GLN
6
L
N
THR
28
B
N
THR
28
L
O
ASN
21
B
O
ASN
21
L
N
PHE
70
B
N
PHE
70
L
O
LEU
65
B
O
LEU
65
L
N
SER
52
B
N
SER
52
L
O
GLU
36
B
O
GLU
36
L
N
LYS
83
B
N
LYS
83
L
O
CYS
80
B
O
CYS
80
L
N
VAL
93
B
N
VAL
93
1
H
ASP
29
70.21
-126.96
1
H
ALA
40
167.49
133.71
1
H
ASN
86
60.83
60.24
1
H
GLN
114
-165.93
112.64
1
H
TYR
123
-119.69
-75.45
1
H
PRO
195
-44.78
-76.25
1
H
TYR
209
-170.17
131.49
1
H
PRO
210
-65.84
-177.93
1
H
LEU
224
-101.76
42.31
1
H
ILE
225
-69.48
61.71
1
H
GLN
226
-147.97
-70.37
1
L
GLU
16
-160.87
104.66
1
L
HIS
31
-171.99
135.11
1
L
LYS
48
-76.20
46.84
PARHCSDX.PRO
TOPHCSDX.PRO
SGH_3.PAR
SGH_3.TOP
WATER_AMMONIA.PAR
TOPH3.CHO
PARAM3_MOD.CHO
WATER_AMMONIA.TOP
30.8
SOME PARAMETER/TOPOLOGY LIBRARIES HAVE BEEN MODIFIED IN-HOUSE TO PROVIDE
MISSING OR CORRECTED SPECIFICATIONS FOR CARBOHYDRATE AND/OR PROTEIN.
0.279
0.005
0.224
0.224
2.2
18.0
2605
26120
10.0
94.0
RANDOM
1
RESTRAINED
THROUGHOUT
0.0
MR
PDB ENTRY 2VAA
0.38
0.30
5
0.53
0.48
2.2
18.0
108
3304
75
0
3121
0.008
1.4
26.2
1.3
2.11
1.50
3.32
2.00
3.43
2.00
4.96
2.50
0.424
0.026
0.368
2.3
266
2374
8
10.0
77.2
34.8
2.1
20.0
1KBG
28511
0
0.078
1
16.2
5.4
89.3
2.1
2.17
1.9
0.384
1
1.7
55.0
data reduction
DENZO
data scaling
SCALEPACK
model building
X-PLOR
refinement
X-PLOR
3.851
phasing
X-PLOR
MHC Class I H-2KB Presented Glycopeptide RGY8-6H-GAL2
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
6
N
N
7
N
N
7
N
N
7
N
N
H
ARG
50
A
ARG
50
HELX_P
H
GLN
54
A
GLN
54
5
1
5
H
PRO
57
A
PRO
57
HELX_P
H
TYR
85
A
TYR
85
1
2
29
H
MET
138
A
MET
138
HELX_P
H
ALA
150
A
ALA
150
1
3
13
H
GLU
152
A
GLU
152
HELX_P
H
GLU
161
A
GLU
161
1
4
10
H
THR
163
A
THR
163
HELX_P
H
ASN
174
A
ASN
174
1
5
12
H
ASN
176
A
ASN
176
HELX_P
H
LEU
179
A
LEU
179
1
6
4
H
GLU
254
A
GLU
254
HELX_P
H
TYR
256
A
TYR
256
5
7
3
disulf
2.033
H
CYS
101
A
SG
CYS
101
1_555
H
CYS
164
A
SG
CYS
164
1_555
disulf
2.028
H
CYS
203
A
SG
CYS
203
1_555
H
CYS
259
A
SG
CYS
259
1_555
disulf
2.027
L
CYS
25
B
SG
CYS
25
1_555
L
CYS
80
B
SG
CYS
80
1_555
covale
1.455
one
N-Glycosylation
H
ASN
86
A
ND2
ASN
86
1_555
H
NAG
1001
F
C1
NAG
1_555
covale
1.451
one
N-Glycosylation
H
ASN
176
A
ND2
ASN
176
1_555
A
NAG
1
D
C1
NAG
1_555
covale
1.324
both
P
TYR
5
C
C
TYR
5
1_555
P
ESC
6
C
N
ESC
6
1_555
covale
1.331
both
P
ESC
6
C
C
ESC
6
1_555
P
GLY
7
C
N
GLY
7
1_555
covale
1.388
one
P
ESC
6
C
CE
ESC
6
1_555
B
GAL
1
E
O1
GAL
1_555
covale
1.389
both
A
NAG
1
D
O4
NAG
1_555
A
NAG
2
D
C1
NAG
1_555
covale
1.401
both
A
NAG
1
D
O6
NAG
1_555
A
FUC
3
D
C1
FUC
1_555
covale
1.395
both
sing
B
GAL
1
E
O4
GAL
1_555
B
GLA
2
E
C1
GLA
1_555
IMMUNE SYSTEM
MHC, MAJOR HISTOCOMPATIBILITY COMPLEX, ANTIGEN PRESENTATION, GLYCOPEPTIDE, CELLULAR IMMUNITY, IMMUNOLOGY, CELL SURFACE RECEPTOR, SYNTHETIC PEPTIDE, VACCINE, IMMUNE SYSTEM
H
TYR
209
A
TYR
209
1
H
PRO
210
A
PRO
210
1.02
L
HIS
31
B
HIS
31
1
L
PRO
32
B
PRO
32
0.31
HA1B_MOUSE
UNP
1
P01901
B2MG_MOUSE
UNP
2
P01887
NCAP_VSVIG
UNP
3
P11212
22
295
1KBG
1
274
P01901
H
1
1
274
21
119
1KBG
1
99
P01887
L
2
1
99
52
59
1KBG
1
8
P11212
P
3
1
8
3
GLN
engineered mutation
ESC
6
1KBG
P
P11212
UNP
57
6
6
2
4
3
4
3
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
H
TYR
45
A
TYR
45
H
PRO
47
A
PRO
47
H
THR
31
A
THR
31
H
ASP
37
A
ASP
37
H
ARG
21
A
ARG
21
H
VAL
28
A
VAL
28
H
HIS
3
A
HIS
3
H
VAL
12
A
VAL
12
H
THR
94
A
THR
94
H
VAL
103
A
VAL
103
H
LEU
109
A
LEU
109
H
TYR
118
A
TYR
118
H
ILE
124
A
ILE
124
H
LEU
126
A
LEU
126
H
TRP
133
A
TRP
133
H
ALA
135
A
ALA
135
H
LYS
186
A
LYS
186
H
ARG
194
A
ARG
194
H
LYS
198
A
LYS
198
H
LEU
206
A
LEU
206
H
LYS
243
A
LYS
243
H
PRO
250
A
PRO
250
H
MET
228
A
MET
228
H
LEU
230
A
LEU
230
H
THR
214
A
THR
214
H
LEU
219
A
LEU
219
H
TYR
257
A
TYR
257
H
TYR
262
A
TYR
262
H
LEU
270
A
LEU
270
H
LEU
272
A
LEU
272
L
GLN
6
B
GLN
6
L
SER
11
B
SER
11
L
PRO
20
B
PRO
20
L
THR
28
B
THR
28
L
ILE
64
B
ILE
64
L
THR
71
B
THR
71
L
GLU
50
B
GLU
50
L
SER
52
B
SER
52
L
GLU
36
B
GLU
36
L
LYS
41
B
LYS
41
L
TYR
78
B
TYR
78
L
LYS
83
B
LYS
83
L
LYS
91
B
LYS
91
L
TYR
94
B
TYR
94
18
P 21 21 2