0.023925
0.000000
0.000000
0.000000
0.009354
0.000000
0.000000
0.000000
0.009086
0.00000
0.00000
0.00000
Giabbai, B.
Sidobre, S.
Crispin, M.M.D.
Sanchez Ruiz, Y.
Bachi, A.
Kronenberg, M.
Wilson, I.A.
Degano, M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
41.798
106.909
110.060
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 H12 O5
164.156
alpha-L-fucopyranose
alpha-L-fucose; 6-deoxy-alpha-L-galactopyranose; L-fucose; fucose
L-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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
non-polymer
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
C45 H90 N O8 P
804.172
7-[(DODECANOYLOXY)METHYL]-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-3,5,8-TRIOXA-4-PHOSPHADOTRIACONTAN-1-AMINIUM 4-OXIDE
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N 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
R
C
N
89
S
C
N
90
R
C
N
91
S
C
N
92
S
C
N
93
N
C
N
94
N
O
N
95
N
O
N
96
N
O
N
97
N
O
N
98
N
O
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
N
N
N
112
S
C
N
113
N
C
N
114
N
O
N
115
N
C
N
116
N
C
N
117
N
C
N
118
N
O
N
119
N
N
N
120
N
O
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
N
N
132
S
C
N
133
N
C
N
134
N
O
N
135
N
C
N
136
N
C
N
137
N
C
N
138
N
O
N
139
N
O
N
140
N
O
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
N
N
151
N
C
N
152
N
C
N
153
N
O
N
154
N
O
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
C
N
161
N
O
N
162
N
C
N
163
N
O
N
164
N
C
N
165
N
O
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
N
N
175
S
C
N
176
N
C
N
177
N
O
N
178
N
C
Y
179
N
C
Y
180
N
N
Y
181
N
C
Y
182
N
C
Y
183
N
N
N
184
N
O
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
O
N
196
N
H
N
197
N
H
N
198
N
N
N
199
S
C
N
200
N
C
N
201
N
O
N
202
S
C
N
203
N
C
N
204
N
C
N
205
N
C
N
206
N
O
N
207
N
H
N
208
N
H
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
H
N
220
N
N
N
221
S
C
N
222
N
C
N
223
N
O
N
224
N
C
N
225
N
C
N
226
N
C
N
227
N
C
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
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
N
N
243
S
C
N
244
N
C
N
245
N
O
N
246
N
C
N
247
N
C
N
248
N
C
N
249
N
C
N
250
N
N
N
251
N
O
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
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
S
C
N
268
S
C
N
269
S
C
N
270
S
C
N
271
R
C
N
272
N
C
N
273
N
O
N
274
N
O
N
275
N
O
N
276
N
O
N
277
N
O
N
278
N
O
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
H
N
289
N
H
N
290
N
H
N
291
N
N
N
292
S
C
N
293
N
C
N
294
N
O
N
295
N
C
N
296
N
C
N
297
N
S
N
298
N
C
N
299
N
O
N
300
N
H
N
301
N
H
N
302
N
H
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
R
C
N
312
R
C
N
313
R
C
N
314
S
C
N
315
R
C
N
316
N
C
N
317
N
C
N
318
N
C
N
319
N
N
N
320
N
O
N
321
N
O
N
322
N
O
N
323
N
O
N
324
N
O
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
N
O
N
342
N
P
N
343
N
O
N
344
N
O
N
345
N
C
N
346
N
C
N
347
N
N
N
348
N
C
N
349
N
C
N
350
N
C
N
351
N
O
N
352
N
C
N
353
R
C
N
354
N
C
N
355
N
O
N
356
N
C
N
357
N
O
N
358
N
C
N
359
N
C
N
360
N
C
N
361
N
C
N
362
N
C
N
363
N
C
N
364
N
C
N
365
N
C
N
366
N
C
N
367
N
C
N
368
N
C
N
369
N
O
N
370
N
C
N
371
N
O
N
372
N
C
N
373
N
C
N
374
N
C
N
375
N
C
N
376
N
C
N
377
N
C
N
378
N
C
N
379
N
C
N
380
N
C
N
381
N
C
N
382
N
C
N
383
N
C
N
384
N
C
N
385
N
C
N
386
N
C
N
387
N
C
N
388
N
C
N
389
N
C
N
390
N
C
N
391
N
C
N
392
N
C
N
393
N
C
N
394
N
C
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
H
N
411
N
H
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
423
N
H
N
424
N
H
N
425
N
H
N
426
N
H
N
427
N
H
N
428
N
H
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
H
N
441
N
H
N
442
N
H
N
443
N
H
N
444
N
H
N
445
N
H
N
446
N
H
N
447
N
H
N
448
N
H
N
449
N
H
N
450
N
H
N
451
N
H
N
452
N
H
N
453
N
H
N
454
N
H
N
455
N
H
N
456
N
H
N
457
N
H
N
458
N
H
N
459
N
H
N
460
N
H
N
461
N
H
N
462
N
H
N
463
N
H
N
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
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
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
N
N
487
S
C
N
488
N
C
N
489
N
O
N
490
N
C
Y
491
N
C
Y
492
N
C
Y
493
N
C
Y
494
N
C
Y
495
N
C
Y
496
N
C
N
497
N
O
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
H
N
506
N
H
N
507
N
H
N
508
N
H
N
509
N
N
N
510
S
C
N
511
N
C
N
512
N
O
N
513
N
C
N
514
N
C
N
515
N
C
N
516
N
O
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
N
C
N
531
N
O
N
532
N
O
N
533
N
H
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
N
N
541
S
C
N
542
N
C
N
543
N
O
N
544
R
C
N
545
N
O
N
546
N
C
N
547
N
O
N
548
N
H
N
549
N
H
N
550
N
H
N
551
N
H
N
552
N
H
N
553
N
H
N
554
N
H
N
555
N
H
N
556
N
H
N
557
N
N
N
558
S
C
N
559
N
C
N
560
N
O
N
561
N
C
Y
562
N
C
Y
563
N
C
Y
564
N
C
Y
565
N
N
Y
566
N
C
Y
567
N
C
Y
568
N
C
Y
569
N
C
Y
570
N
C
N
571
N
O
N
572
N
H
N
573
N
H
N
574
N
H
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
C
Y
593
N
C
Y
594
N
C
N
595
N
O
N
596
N
O
N
597
N
H
N
598
N
H
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
N
N
609
S
C
N
610
N
C
N
611
N
O
N
612
N
C
N
613
N
C
N
614
N
C
N
615
N
O
N
616
N
H
N
617
N
H
N
618
N
H
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
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
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
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
doub
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
doub
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
doub
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
doub
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
doub
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
Y
176
N
sing
Y
177
N
doub
Y
178
N
doub
N
179
N
sing
Y
180
N
sing
N
181
N
sing
Y
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
N
191
N
sing
N
192
N
sing
N
193
N
sing
N
194
N
doub
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
sing
N
202
N
sing
N
203
N
sing
N
204
N
sing
N
205
N
sing
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
doub
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
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
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
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
sing
N
262
N
sing
N
263
N
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
doub
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
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
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
doub
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
doub
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
sing
N
359
N
sing
N
360
N
sing
N
361
N
doub
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
doub
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
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
sing
N
433
N
sing
N
434
N
sing
N
435
N
sing
N
436
N
sing
N
437
N
sing
N
438
N
sing
N
439
N
sing
N
440
N
sing
N
441
N
sing
N
442
N
sing
N
443
N
sing
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
N
448
N
sing
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
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
sing
N
469
N
sing
N
470
N
sing
N
471
N
sing
N
472
N
sing
N
473
N
sing
N
474
N
sing
N
475
N
sing
N
476
N
sing
N
477
N
doub
N
478
N
sing
N
479
N
sing
N
480
N
sing
N
481
N
sing
Y
482
N
doub
Y
483
N
sing
Y
484
N
sing
N
485
N
sing
Y
486
N
doub
N
487
N
sing
Y
488
N
doub
N
489
N
sing
Y
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
doub
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
doub
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
doub
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
sing
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
doub
N
547
N
sing
N
548
N
sing
N
549
N
sing
N
550
N
sing
Y
551
N
doub
Y
552
N
sing
Y
553
N
sing
N
554
N
sing
Y
555
N
doub
Y
556
N
sing
Y
557
N
sing
N
558
N
sing
Y
559
N
sing
Y
560
N
doub
N
561
N
sing
Y
562
N
doub
N
563
N
sing
Y
564
N
sing
N
565
N
sing
N
566
N
sing
N
567
N
sing
N
568
N
sing
N
569
N
sing
N
570
N
sing
N
571
N
sing
N
572
N
sing
N
573
N
sing
N
574
N
doub
N
575
N
sing
N
576
N
sing
N
577
N
sing
N
578
N
sing
Y
579
N
doub
Y
580
N
sing
Y
581
N
sing
N
582
N
sing
Y
583
N
doub
N
584
N
sing
Y
585
N
doub
N
586
N
sing
Y
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
doub
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
US
J.Immunol.
JOIMA3
0952
0022-1767
175
977
984
16002697
Crystal structure of mouse CD1d bound to the self ligand phosphatidylcholine: a molecular basis for NKT cell activation
2005
US
Science
SCIEAS
0038
0036-8075
277
339
345
Crystal structure of mouse CD1: An MHC-like fold with a large hydrophobic binding groove
1997
10.2210/pdb1zhn/pdb
pdb_00001zhn
NAG C 1 HAS WRONG CHIRALITY AT ATOM C1
MAN D 3 HAS WRONG CHIRALITY AT ATOM C1
100
1
IMAGE PLATE
1998-05-22
MARRESEARCH
Mirrors
SINGLE WAVELENGTH
M
x-ray
1
1.0000
1.0
BL7-1
SSRL
1.0000
SYNCHROTRON
SSRL BEAMLINE BL7-1
Self phospholipid copurified with protein
31131.100
CD1d1 antigen
1
man
polymer
11704.359
beta-2-microglobulin
1
man
polymer
367.349
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose
1
man
branched
1056.964
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose
1
man
branched
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
1
man
non-polymer
804.172
7-[(DODECANOYLOXY)METHYL]-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-3,5,8-TRIOXA-4-PHOSPHADOTRIACONTAN-1-AMINIUM 4-OXIDE
1
syn
non-polymer
92.094
GLYCEROL
1
syn
non-polymer
18.015
water
50
nat
water
T-cell surface glycoprotein CD1d1
no
no
NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVK
MMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLND
TCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWY
LQATLDVEAGEEAGLACRVKHSSLGGQDIILYW
NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVK
MMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLND
TCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWY
LQATLDVEAGEEAGLACRVKHSSLGGQDIILYW
A
polypeptide(L)
no
no
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYAC
RVKHDSMAEPKTVYWDRDM
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYAC
RVKHDSMAEPKTVYWDRDM
B
polypeptide(L)
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
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
fruit fly
Drosophila
sample
10090
Mus musculus
S2 cells
7227
Drosophila melanogaster
pRmHa-3
house mouse
Mus
fruit fly
Drosophila
sample
10090
Mus musculus
S2 cells
7227
Drosophila melanogaster
pRmHa-3
1
2.9
57.7
VAPOR DIFFUSION, HANGING DROP
7.4
100 mM Tris, 200 mM NH4(SO4)2, 25% PEG 4000, pH 7.4, VAPOR DIFFUSION, HANGING DROP, temperature 293K
293
atom_site
chem_comp
database_PDB_caveat
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
pdbx_validate_chiral
struct_asym
struct_conn
struct_site
struct_site_gen
chem_comp
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Non-polymer description
Version format compliance
Advisory
Atomic model
Data collection
Derived calculations
Structure summary
Data collection
Database references
Refinement description
Structure summary
1
0
2005-07-19
1
1
2008-04-30
1
2
2011-07-13
2
0
2020-07-29
2
1
2023-08-23
_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
_entity.formula_weight
_entity.pdbx_description
_entity.pdbx_number_of_molecules
_entity.type
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_validate_chiral.auth_asym_id
_pdbx_validate_chiral.auth_seq_id
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_struct_conn.pdbx_role
_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
C
NAG
1
n
C
NAG
1
C
FUC
13
n
C
FUC
2
E
NAG
3
n
D
NAG
1
E
NAG
31
n
D
NAG
2
E
MAN
32
n
D
MAN
3
E
MAN
33
n
D
MAN
4
E
MAN
34
n
D
MAN
5
E
FUC
35
n
D
FUC
6
LFucpa
a-L-fucopyranose
a-L-Fucp
Fuc
DManpa
a-D-mannopyranose
a-D-Manp
Man
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
Mouse CD1d with no ligand
Human CD1b bound to PI
Human CD1b bound to GM1
Human CD1a bound to sulfatide self ligand
N
RCSB
Y
RCSB
2005-04-26
REL
REL
oligosaccharide
oligosaccharide
LFucpa1-6DGlcpNAcb1-
3
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/2,2,1/[a2122h-1b_1-5_2*NCC/3=O][a1221m-1a_1-5]/1-2/a6-b1
3
PDB2Glycan
1.1.0
WURCS
[]{[(4+1)][a-D-GlcpNAc]{[(6+1)][a-L-Fucp]{}}}
3
PDB-CARE
LINUCS
DManpa1-3[DManpa1-6]DManpa1-4DGlcpNAcb1-4[LFucpa1-6]DGlcpNAcb1-
4
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/3,6,5/[a2122h-1b_1-5_2*NCC/3=O][a1122h-1a_1-5][a1221m-1a_1-5]/1-1-2-2-2-3/a4-b1_a6-f1_b4-c1_c3-d1_c6-e1
4
PDB2Glycan
1.1.0
WURCS
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-Manp]{[(3+1)][a-D-Manp]{}[(6+1)][a-D-Manp]{}}}[(6+1)][a-L-Fucp]{}}}
4
PDB-CARE
LINUCS
C1
O6
FUC
NAG
2
1
3
O1
HO6
sing
C1
O4
NAG
NAG
2
1
4
O1
HO4
sing
C1
O4
MAN
NAG
3
2
4
O1
HO4
sing
C1
O3
MAN
MAN
4
3
4
O1
HO3
sing
C1
O6
MAN
MAN
5
3
4
O1
HO6
sing
C1
O6
FUC
NAG
6
1
4
O1
HO6
sing
n
n
n
n
n
n
n
n
NAG
2-acetamido-2-deoxy-beta-D-glucopyranose
PC6
7-[(DODECANOYLOXY)METHYL]-4-HYDROXY-N,N,N-TRIMETHYL-9-OXO-3,5,8-TRIOXA-4-PHOSPHADOTRIACONTAN-1-AMINIUM 4-OXIDE
GOL
GLYCEROL
HOH
water
1CD1
PDB
experimental model
NAG
2
5
NAG
NAG
2
A
PC6
1
6
PC6
PC6
1
A
GOL
2002
7
GOL
GOL
2002
B
HOH
3
8
HOH
HOH
288
A
HOH
6
8
HOH
HOH
289
A
HOH
8
8
HOH
HOH
290
A
HOH
12
8
HOH
HOH
291
A
HOH
18
8
HOH
HOH
292
A
HOH
20
8
HOH
HOH
293
A
HOH
22
8
HOH
HOH
294
A
HOH
24
8
HOH
HOH
295
A
HOH
28
8
HOH
HOH
296
A
HOH
30
8
HOH
HOH
297
A
HOH
31
8
HOH
HOH
298
A
HOH
32
8
HOH
HOH
299
A
HOH
36
8
HOH
HOH
300
A
HOH
37
8
HOH
HOH
301
A
HOH
38
8
HOH
HOH
302
A
HOH
45
8
HOH
HOH
303
A
HOH
48
8
HOH
HOH
304
A
HOH
49
8
HOH
HOH
305
A
HOH
50
8
HOH
HOH
306
A
HOH
51
8
HOH
HOH
307
A
HOH
52
8
HOH
HOH
308
A
HOH
53
8
HOH
HOH
309
A
HOH
54
8
HOH
HOH
310
A
HOH
55
8
HOH
HOH
311
A
HOH
57
8
HOH
HOH
312
A
HOH
58
8
HOH
HOH
313
A
HOH
59
8
HOH
HOH
314
A
HOH
61
8
HOH
HOH
315
A
HOH
63
8
HOH
HOH
316
A
HOH
66
8
HOH
HOH
317
A
HOH
67
8
HOH
HOH
318
A
HOH
68
8
HOH
HOH
319
A
HOH
69
8
HOH
HOH
320
A
HOH
2
8
HOH
HOH
2003
B
HOH
4
8
HOH
HOH
2004
B
HOH
13
8
HOH
HOH
2005
B
HOH
15
8
HOH
HOH
2006
B
HOH
17
8
HOH
HOH
2007
B
HOH
21
8
HOH
HOH
2008
B
HOH
25
8
HOH
HOH
2009
B
HOH
27
8
HOH
HOH
2010
B
HOH
29
8
HOH
HOH
2011
B
HOH
33
8
HOH
HOH
2012
B
HOH
35
8
HOH
HOH
2013
B
HOH
40
8
HOH
HOH
2014
B
HOH
41
8
HOH
HOH
2015
B
HOH
46
8
HOH
HOH
2016
B
HOH
56
8
HOH
HOH
2017
B
HOH
62
8
HOH
HOH
2018
B
HOH
64
8
HOH
HOH
2019
B
ASN
7
n
1
ASN
7
A
TYR
8
n
2
TYR
8
A
THR
9
n
3
THR
9
A
PHE
10
n
4
PHE
10
A
ARG
11
n
5
ARG
11
A
CYS
12
n
6
CYS
12
A
LEU
13
n
7
LEU
13
A
GLN
14
n
8
GLN
14
A
MET
15
n
9
MET
15
A
SER
16
n
10
SER
16
A
SER
17
n
11
SER
17
A
PHE
18
n
12
PHE
18
A
ALA
19
n
13
ALA
19
A
ASN
20
n
14
ASN
20
A
ARG
21
n
15
ARG
21
A
SER
22
n
16
SER
22
A
TRP
23
n
17
TRP
23
A
SER
24
n
18
SER
24
A
ARG
25
n
19
ARG
25
A
THR
26
n
20
THR
26
A
ASP
27
n
21
ASP
27
A
SER
28
n
22
SER
28
A
VAL
29
n
23
VAL
29
A
VAL
30
n
24
VAL
30
A
TRP
31
n
25
TRP
31
A
LEU
32
n
26
LEU
32
A
GLY
33
n
27
GLY
33
A
ASP
34
n
28
ASP
34
A
LEU
35
n
29
LEU
35
A
GLN
36
n
30
GLN
36
A
THR
37
n
31
THR
37
A
HIS
38
n
32
HIS
38
A
ARG
39
n
33
ARG
39
A
TRP
40
n
34
TRP
40
A
SER
41
n
35
SER
41
A
ASN
42
n
36
ASN
42
A
ASP
43
n
37
ASP
43
A
SER
44
n
38
SER
44
A
ALA
45
n
39
ALA
45
A
THR
46
n
40
THR
46
A
ILE
47
n
41
ILE
47
A
SER
48
n
42
SER
48
A
PHE
49
n
43
PHE
49
A
THR
50
n
44
THR
50
A
LYS
51
n
45
LYS
51
A
PRO
52
n
46
PRO
52
A
TRP
53
n
47
TRP
53
A
SER
54
n
48
SER
54
A
GLN
55
n
49
GLN
55
A
GLY
56
n
50
GLY
56
A
LYS
57
n
51
LYS
57
A
LEU
58
n
52
LEU
58
A
SER
59
n
53
SER
59
A
ASN
60
n
54
ASN
60
A
GLN
61
n
55
GLN
61
A
GLN
62
n
56
GLN
62
A
TRP
63
n
57
TRP
63
A
GLU
64
n
58
GLU
64
A
LYS
65
n
59
LYS
65
A
LEU
66
n
60
LEU
66
A
GLN
67
n
61
GLN
67
A
HIS
68
n
62
HIS
68
A
MET
69
n
63
MET
69
A
PHE
70
n
64
PHE
70
A
GLN
71
n
65
GLN
71
A
VAL
72
n
66
VAL
72
A
TYR
73
n
67
TYR
73
A
ARG
74
n
68
ARG
74
A
VAL
75
n
69
VAL
75
A
SER
76
n
70
SER
76
A
PHE
77
n
71
PHE
77
A
THR
78
n
72
THR
78
A
ARG
79
n
73
ARG
79
A
ASP
80
n
74
ASP
80
A
ILE
81
n
75
ILE
81
A
GLN
82
n
76
GLN
82
A
GLU
83
n
77
GLU
83
A
LEU
84
n
78
LEU
84
A
VAL
85
n
79
VAL
85
A
LYS
86
n
80
LYS
86
A
MET
87
n
81
MET
87
A
MET
88
n
82
MET
88
A
SER
89
n
83
SER
89
A
PRO
90
n
84
PRO
90
A
LYS
91
n
85
LYS
91
A
GLU
92
n
86
GLU
92
A
n
87
93
A
n
88
94
A
n
89
95
A
ILE
96
n
90
ILE
96
A
GLU
97
n
91
GLU
97
A
ILE
98
n
92
ILE
98
A
GLN
99
n
93
GLN
99
A
LEU
100
n
94
LEU
100
A
SER
101
n
95
SER
101
A
ALA
102
n
96
ALA
102
A
GLY
103
n
97
GLY
103
A
CYS
104
n
98
CYS
104
A
GLU
105
n
99
GLU
105
A
MET
106
n
100
MET
106
A
TYR
107
n
101
TYR
107
A
PRO
108
n
102
PRO
108
A
GLY
109
n
103
GLY
109
A
ASN
110
n
104
ASN
110
A
ALA
111
n
105
ALA
111
A
SER
112
n
106
SER
112
A
GLU
113
n
107
GLU
113
A
SER
114
n
108
SER
114
A
PHE
115
n
109
PHE
115
A
LEU
116
n
110
LEU
116
A
HIS
117
n
111
HIS
117
A
VAL
118
n
112
VAL
118
A
ALA
119
n
113
ALA
119
A
PHE
120
n
114
PHE
120
A
GLN
121
n
115
GLN
121
A
GLY
122
n
116
GLY
122
A
LYS
123
n
117
LYS
123
A
TYR
124
n
118
TYR
124
A
VAL
125
n
119
VAL
125
A
VAL
126
n
120
VAL
126
A
ARG
127
n
121
ARG
127
A
PHE
128
n
122
PHE
128
A
TRP
129
n
123
TRP
129
A
GLY
130
n
124
GLY
130
A
THR
131
n
125
THR
131
A
SER
132
n
126
SER
132
A
TRP
133
n
127
TRP
133
A
GLN
134
n
128
GLN
134
A
THR
135
n
129
THR
135
A
VAL
136
n
130
VAL
136
A
PRO
137
n
131
PRO
137
A
GLY
138
n
132
GLY
138
A
ALA
139
n
133
ALA
139
A
PRO
140
n
134
PRO
140
A
SER
141
n
135
SER
141
A
TRP
142
n
136
TRP
142
A
LEU
143
n
137
LEU
143
A
ASP
144
n
138
ASP
144
A
LEU
145
n
139
LEU
145
A
PRO
146
n
140
PRO
146
A
ILE
147
n
141
ILE
147
A
LYS
148
n
142
LYS
148
A
VAL
149
n
143
VAL
149
A
LEU
150
n
144
LEU
150
A
ASN
151
n
145
ASN
151
A
ALA
152
n
146
ALA
152
A
ASP
153
n
147
ASP
153
A
GLN
154
n
148
GLN
154
A
GLY
155
n
149
GLY
155
A
THR
156
n
150
THR
156
A
SER
157
n
151
SER
157
A
ALA
158
n
152
ALA
158
A
THR
159
n
153
THR
159
A
VAL
160
n
154
VAL
160
A
GLN
161
n
155
GLN
161
A
MET
162
n
156
MET
162
A
LEU
163
n
157
LEU
163
A
LEU
164
n
158
LEU
164
A
ASN
165
n
159
ASN
165
A
ASP
166
n
160
ASP
166
A
THR
167
n
161
THR
167
A
CYS
168
n
162
CYS
168
A
PRO
169
n
163
PRO
169
A
LEU
170
n
164
LEU
170
A
PHE
171
n
165
PHE
171
A
VAL
172
n
166
VAL
172
A
ARG
173
n
167
ARG
173
A
GLY
174
n
168
GLY
174
A
LEU
175
n
169
LEU
175
A
LEU
176
n
170
LEU
176
A
GLU
177
n
171
GLU
177
A
ALA
178
n
172
ALA
178
A
GLY
179
n
173
GLY
179
A
LYS
180
n
174
LYS
180
A
SER
181
n
175
SER
181
A
ASP
182
n
176
ASP
182
A
LEU
183
n
177
LEU
183
A
GLU
184
n
178
GLU
184
A
LYS
185
n
179
LYS
185
A
GLN
186
n
180
GLN
186
A
GLU
187
n
181
GLU
187
A
LYS
188
n
182
LYS
188
A
PRO
189
n
183
PRO
189
A
VAL
190
n
184
VAL
190
A
ALA
191
n
185
ALA
191
A
TRP
192
n
186
TRP
192
A
LEU
193
n
187
LEU
193
A
SER
194
n
188
SER
194
A
SER
195
n
189
SER
195
A
VAL
196
n
190
VAL
196
A
PRO
197
n
191
PRO
197
A
SER
198
n
192
SER
198
A
SER
199
n
193
SER
199
A
ALA
200
n
194
ALA
200
A
HIS
201
n
195
HIS
201
A
GLY
202
n
196
GLY
202
A
HIS
203
n
197
HIS
203
A
ARG
204
n
198
ARG
204
A
GLN
205
n
199
GLN
205
A
LEU
206
n
200
LEU
206
A
VAL
207
n
201
VAL
207
A
CYS
208
n
202
CYS
208
A
HIS
209
n
203
HIS
209
A
VAL
210
n
204
VAL
210
A
SER
211
n
205
SER
211
A
GLY
212
n
206
GLY
212
A
PHE
213
n
207
PHE
213
A
TYR
214
n
208
TYR
214
A
PRO
215
n
209
PRO
215
A
LYS
216
n
210
LYS
216
A
PRO
217
n
211
PRO
217
A
VAL
218
n
212
VAL
218
A
TRP
219
n
213
TRP
219
A
VAL
220
n
214
VAL
220
A
MET
221
n
215
MET
221
A
TRP
222
n
216
TRP
222
A
MET
223
n
217
MET
223
A
ARG
224
n
218
ARG
224
A
GLY
225
n
219
GLY
225
A
ASP
226
n
220
ASP
226
A
GLN
227
n
221
GLN
227
A
GLU
228
n
222
GLU
228
A
GLN
229
n
223
GLN
229
A
GLN
230
n
224
GLN
230
A
GLY
231
n
225
GLY
231
A
THR
232
n
226
THR
232
A
HIS
233
n
227
HIS
233
A
ARG
234
n
228
ARG
234
A
GLY
235
n
229
GLY
235
A
ASP
236
n
230
ASP
236
A
PHE
237
n
231
PHE
237
A
LEU
238
n
232
LEU
238
A
PRO
239
n
233
PRO
239
A
ASN
240
n
234
ASN
240
A
ALA
241
n
235
ALA
241
A
ASP
242
n
236
ASP
242
A
GLU
243
n
237
GLU
243
A
THR
244
n
238
THR
244
A
TRP
245
n
239
TRP
245
A
TYR
246
n
240
TYR
246
A
LEU
247
n
241
LEU
247
A
GLN
248
n
242
GLN
248
A
ALA
249
n
243
ALA
249
A
THR
250
n
244
THR
250
A
LEU
251
n
245
LEU
251
A
ASP
252
n
246
ASP
252
A
VAL
253
n
247
VAL
253
A
GLU
254
n
248
GLU
254
A
ALA
255
n
249
ALA
255
A
GLY
256
n
250
GLY
256
A
GLU
257
n
251
GLU
257
A
GLU
258
n
252
GLU
258
A
ALA
259
n
253
ALA
259
A
GLY
260
n
254
GLY
260
A
LEU
261
n
255
LEU
261
A
ALA
262
n
256
ALA
262
A
CYS
263
n
257
CYS
263
A
ARG
264
n
258
ARG
264
A
VAL
265
n
259
VAL
265
A
LYS
266
n
260
LYS
266
A
HIS
267
n
261
HIS
267
A
SER
268
n
262
SER
268
A
SER
269
n
263
SER
269
A
LEU
270
n
264
LEU
270
A
GLY
271
n
265
GLY
271
A
GLY
272
n
266
GLY
272
A
GLN
273
n
267
GLN
273
A
ASP
274
n
268
ASP
274
A
ILE
275
n
269
ILE
275
A
ILE
276
n
270
ILE
276
A
LEU
277
n
271
LEU
277
A
TYR
278
n
272
TYR
278
A
TRP
279
n
273
TRP
279
A
ILE
1
n
1
ILE
1
B
GLN
2
n
2
GLN
2
B
LYS
3
n
3
LYS
3
B
THR
4
n
4
THR
4
B
PRO
5
n
5
PRO
5
B
GLN
6
n
6
GLN
6
B
ILE
7
n
7
ILE
7
B
GLN
8
n
8
GLN
8
B
VAL
9
n
9
VAL
9
B
TYR
10
n
10
TYR
10
B
SER
11
n
11
SER
11
B
ARG
12
n
12
ARG
12
B
HIS
13
n
13
HIS
13
B
PRO
14
n
14
PRO
14
B
PRO
15
n
15
PRO
15
B
GLU
16
n
16
GLU
16
B
ASN
17
n
17
ASN
17
B
GLY
18
n
18
GLY
18
B
LYS
19
n
19
LYS
19
B
PRO
20
n
20
PRO
20
B
ASN
21
n
21
ASN
21
B
ILE
22
n
22
ILE
22
B
LEU
23
n
23
LEU
23
B
ASN
24
n
24
ASN
24
B
CYS
25
n
25
CYS
25
B
TYR
26
n
26
TYR
26
B
VAL
27
n
27
VAL
27
B
THR
28
n
28
THR
28
B
GLN
29
n
29
GLN
29
B
PHE
30
n
30
PHE
30
B
HIS
31
n
31
HIS
31
B
PRO
32
n
32
PRO
32
B
PRO
33
n
33
PRO
33
B
HIS
34
n
34
HIS
34
B
ILE
35
n
35
ILE
35
B
GLU
36
n
36
GLU
36
B
ILE
37
n
37
ILE
37
B
GLN
38
n
38
GLN
38
B
MET
39
n
39
MET
39
B
LEU
40
n
40
LEU
40
B
LYS
41
n
41
LYS
41
B
ASN
42
n
42
ASN
42
B
GLY
43
n
43
GLY
43
B
LYS
44
n
44
LYS
44
B
LYS
45
n
45
LYS
45
B
ILE
46
n
46
ILE
46
B
PRO
47
n
47
PRO
47
B
LYS
48
n
48
LYS
48
B
VAL
49
n
49
VAL
49
B
GLU
50
n
50
GLU
50
B
MET
51
n
51
MET
51
B
SER
52
n
52
SER
52
B
ASP
53
n
53
ASP
53
B
MET
54
n
54
MET
54
B
SER
55
n
55
SER
55
B
PHE
56
n
56
PHE
56
B
SER
57
n
57
SER
57
B
LYS
58
n
58
LYS
58
B
ASP
59
n
59
ASP
59
B
TRP
60
n
60
TRP
60
B
SER
61
n
61
SER
61
B
PHE
62
n
62
PHE
62
B
TYR
63
n
63
TYR
63
B
ILE
64
n
64
ILE
64
B
LEU
65
n
65
LEU
65
B
ALA
66
n
66
ALA
66
B
HIS
67
n
67
HIS
67
B
THR
68
n
68
THR
68
B
GLU
69
n
69
GLU
69
B
PHE
70
n
70
PHE
70
B
THR
71
n
71
THR
71
B
PRO
72
n
72
PRO
72
B
THR
73
n
73
THR
73
B
GLU
74
n
74
GLU
74
B
THR
75
n
75
THR
75
B
ASP
76
n
76
ASP
76
B
THR
77
n
77
THR
77
B
TYR
78
n
78
TYR
78
B
ALA
79
n
79
ALA
79
B
CYS
80
n
80
CYS
80
B
ARG
81
n
81
ARG
81
B
VAL
82
n
82
VAL
82
B
LYS
83
n
83
LYS
83
B
HIS
84
n
84
HIS
84
B
ASP
85
n
85
ASP
85
B
SER
86
n
86
SER
86
B
MET
87
n
87
MET
87
B
ALA
88
n
88
ALA
88
B
GLU
89
n
89
GLU
89
B
PRO
90
n
90
PRO
90
B
LYS
91
n
91
LYS
91
B
THR
92
n
92
THR
92
B
VAL
93
n
93
VAL
93
B
TYR
94
n
94
TYR
94
B
TRP
95
n
95
TRP
95
B
ASP
96
n
96
ASP
96
B
ARG
97
n
97
ARG
97
B
ASP
98
n
98
ASP
98
B
MET
99
n
99
MET
99
B
author_and_software_defined_assembly
PISA
2
dimeric
7160
5
19160
A
ASN
20
GLYCOSYLATION SITE
A
ASN
14
ASN
A
ASN
42
GLYCOSYLATION SITE
A
ASN
36
ASN
A
ASN
165
GLYCOSYLATION SITE
A
ASN
159
ASN
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
1_555
x,y,z
identity operation
0.0000000000
0.0000000000
0.0000000000
A
O
SER
48
A
O
SER
42
A
N
ARG
39
A
N
ARG
33
A
O
LEU
35
A
O
LEU
29
A
N
LEU
32
A
N
LEU
26
A
O
ARG
25
A
O
ARG
19
A
N
SER
17
A
N
SER
11
A
N
CYS
12
A
N
CYS
6
A
O
ALA
102
A
O
ALA
96
A
N
GLY
103
A
N
GLY
97
A
O
PHE
115
A
O
PHE
109
A
N
VAL
118
A
N
VAL
112
A
O
VAL
126
A
O
VAL
120
A
N
TRP
129
A
N
TRP
123
A
O
SER
132
A
O
SER
126
A
N
SER
194
A
N
SER
188
A
O
VAL
207
A
O
VAL
201
A
N
ARG
204
A
N
ARG
198
A
O
VAL
253
A
O
VAL
247
A
O
THR
250
A
O
THR
244
A
N
HIS
233
A
N
HIS
227
A
N
SER
194
A
N
SER
188
A
O
VAL
207
A
O
VAL
201
A
N
ARG
204
A
N
ARG
198
A
O
VAL
253
A
O
VAL
247
A
O
TYR
246
A
O
TYR
240
A
N
LEU
238
A
N
LEU
232
A
O
GLN
227
A
O
GLN
221
A
N
ARG
224
A
N
ARG
218
A
N
MET
223
A
N
MET
217
A
O
ALA
262
A
O
ALA
256
A
N
VAL
265
A
N
VAL
259
A
O
ILE
275
A
O
ILE
269
B
N
GLN
8
B
N
GLN
8
B
O
TYR
26
B
O
TYR
26
B
N
CYS
25
B
N
CYS
25
B
O
ALA
66
B
O
ALA
66
B
O
HIS
67
B
O
HIS
67
B
N
GLU
50
B
N
GLU
50
B
N
GLN
8
B
N
GLN
8
B
O
TYR
26
B
O
TYR
26
B
N
CYS
25
B
N
CYS
25
B
O
ALA
66
B
O
ALA
66
B
O
TYR
63
B
O
TYR
63
B
N
SER
55
B
N
SER
55
B
O
LYS
44
B
O
LYS
44
B
N
LYS
41
B
N
LYS
41
B
N
GLN
38
B
N
GLN
38
B
O
ARG
81
B
O
ARG
81
B
N
VAL
82
B
N
VAL
82
B
O
LYS
91
B
O
LYS
91
1
A
ASP
93
A
ASP
87
1
Y
1
A
TYR
94
A
TYR
88
1
Y
1
A
PRO
95
A
PRO
89
1
Y
1
C
C1
NAG
1
WRONG HAND
1
D
C1
MAN
3
WRONG HAND
1
A
A
O
O
HOH
HOH
289
293
2.08
1
A
A
SER
PRO
89
90
145.34
1
6.02
0.90
118.30
124.32
A
A
A
CB
CG
OD2
ASP
ASP
ASP
34
34
34
N
1
5.62
0.90
118.30
123.92
B
B
B
CB
CG
OD2
ASP
ASP
ASP
98
98
98
N
1
A
ASN
20
-127.54
-145.81
1
A
SER
89
47.70
-144.53
1
A
LYS
91
178.84
107.58
1
A
LEU
116
-161.54
115.23
1
A
VAL
125
-130.99
-36.81
1
A
ASP
166
-105.64
-66.49
1
B
HIS
31
-175.41
136.46
1
B
LYS
48
-95.30
30.49
1
B
TRP
60
72.48
-15.88
25.724
-1.34
0.00
0.00
-1.16
0.00
2.50
0.896
0.838
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
0.28097
0.21632
0.22174
0.22174
2.80
76.70
1018
11481
11481
8.1
98.15
16.190
0.309
RANDOM
1
THROUGHOUT
0
MOLECULAR REPLACEMENT
0.430
0.80
0.80
1.20
1CD1
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
2.80
76.70
50
3207
170
0
2987
0.005
0.021
3255
0.001
0.020
2836
1.473
1.971
4423
0.766
3.000
6614
7.160
5.000
366
35.718
24.178
146
18.958
15.000
514
23.189
15.000
15
0.078
0.200
481
0.004
0.020
3423
0.001
0.020
629
0.209
0.200
687
0.186
0.200
3012
0.189
0.200
1537
0.089
0.200
2029
0.178
0.200
86
0.110
0.200
10
0.204
0.200
42
0.170
0.200
5
0.688
1.500
2385
0.067
1.500
742
0.773
2.000
2989
0.957
3.000
1665
1.722
4.500
1434
0.385
0.302
2.873
71
792
20
95.57
39.3
2.80
76.70
1ZHN
12734
12734
-3.0
0.056
1
8.4
4.3
98.1
2.80
2.95
2.5
1810
0.29
1
4.0
96.0
data reduction
MOSFLM
data scaling
SCALA
phasing
MOLREP
refinement
REFMAC
5.2
data scaling
CCP4
(SCALA)
Crystal Structure of mouse CD1d bound to the self ligand phosphatidylcholine
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
6
N
N
7
N
N
8
N
N
8
N
N
The biological assembly is a heterodimeric CD1d/beta-2microglobulin complex bound to one PC molecule, as found in the crystal asymmetric unit
A
SER
59
A
SER
53
HELX_P
A
MET
87
A
MET
81
1
1
29
A
PRO
140
A
PRO
134
HELX_P
A
TRP
142
A
TRP
136
5
2
3
A
LEU
143
A
LEU
137
HELX_P
A
ASP
153
A
ASP
147
1
3
11
A
ASP
153
A
ASP
147
HELX_P
A
ASP
166
A
ASP
160
1
4
14
A
ASP
166
A
ASP
160
HELX_P
A
GLY
179
A
GLY
173
1
5
14
A
GLY
179
A
GLY
173
HELX_P
A
GLU
184
A
GLU
178
1
6
6
A
HIS
267
A
HIS
261
HELX_P
A
GLY
271
A
GLY
265
5
7
5
disulf
2.041
A
CYS
104
A
SG
CYS
98
1_555
A
CYS
168
A
SG
CYS
162
1_555
disulf
2.030
A
CYS
208
A
SG
CYS
202
1_555
A
CYS
263
A
SG
CYS
257
1_555
disulf
2.028
B
CYS
25
B
SG
CYS
25
1_555
B
CYS
80
B
SG
CYS
80
1_555
covale
1.447
one
N-Glycosylation
A
NAG
2
E
C1
NAG
1_555
A
ASN
42
A
ND2
ASN
36
1_555
covale
1.445
one
N-Glycosylation
A
ASN
20
A
ND2
ASN
14
1_555
C
NAG
1
C
C1
NAG
1_555
covale
1.442
one
N-Glycosylation
A
ASN
165
A
ND2
ASN
159
1_555
D
NAG
1
D
C1
NAG
1_555
covale
1.446
both
C
NAG
1
C
O6
NAG
1_555
C
FUC
2
C
C1
FUC
1_555
covale
1.435
both
D
NAG
1
D
O4
NAG
1_555
D
NAG
2
D
C1
NAG
1_555
covale
1.452
both
D
NAG
1
D
O6
NAG
1_555
D
FUC
6
D
C1
FUC
1_555
covale
1.447
both
D
NAG
2
D
O4
NAG
1_555
D
MAN
3
D
C1
MAN
1_555
covale
1.441
both
D
MAN
3
D
O3
MAN
1_555
D
MAN
4
D
C1
MAN
1_555
covale
1.446
both
D
MAN
3
D
O6
MAN
1_555
D
MAN
5
D
C1
MAN
1_555
IMMUNE SYSTEM, MEMBRANE PROTEIN
MHC fold; antigen binding domain; Ig fold, IMMUNE SYSTEM, MEMBRANE PROTEIN
A
TYR
214
A
TYR
208
1
A
PRO
215
A
PRO
209
-1.45
B
HIS
31
B
HIS
31
1
B
PRO
32
B
PRO
32
5.13
BAB22206
GB
1
25
12832671
NYTFRCLQMSSFANRSWSRTDSVVWLGDLQTHRWSNDSATISFTKPWSQGKLSNQQWEKLQHMFQVYRVSFTRDIQELVK
MMSPKEDYPIEIQLSAGCEMYPGNASESFLHVAFQGKYVVRFWGTSWQTVPGAPSWLDLPIKVLNADQGTSATVQMLLND
TCPLFVRGLLEAGKSDLEKQEKPVAWLSSVPSSAHGHRQLVCHVSGFYPKPVWVMWMRGDQEQQGTHRGDFLPNADETWY
LQATLDVEAGEEAGLACRVKHSSLGGQDIILYW
B2MG_MOUSE
UNP
2
21
P01887
IQKTPQIQVYSRHPPENGKPNILNCYVTQFHPPHIEIQMLKNGKKIPKVEMSDMSFSKDWSFYILAHTEFTPTETDTYAC
RVKHDSMAEPKTVYWDRDM
25
297
1ZHN
7
279
12832671
A
1
1
273
21
119
1ZHN
1
99
P01887
B
2
1
99
8
4
4
4
4
4
4
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
SER
48
A
SER
42
A
PHE
49
A
PHE
43
A
LEU
35
A
LEU
29
A
TRP
40
A
TRP
34
A
SER
24
A
SER
18
A
LEU
32
A
LEU
26
A
TYR
8
A
TYR
2
A
PHE
18
A
PHE
12
A
GLU
97
A
GLU
91
A
TYR
107
A
TYR
101
A
ALA
111
A
ALA
105
A
PHE
120
A
PHE
114
A
LYS
123
A
LYS
117
A
TRP
129
A
TRP
123
A
SER
132
A
SER
126
A
THR
135
A
THR
129
A
VAL
190
A
VAL
184
A
PRO
197
A
PRO
191
A
HIS
203
A
HIS
197
A
PHE
213
A
PHE
207
A
TRP
245
A
TRP
239
A
GLU
254
A
GLU
248
A
HIS
233
A
HIS
227
A
ARG
234
A
ARG
228
A
VAL
190
A
VAL
184
A
PRO
197
A
PRO
191
A
HIS
203
A
HIS
197
A
PHE
213
A
PHE
207
A
TRP
245
A
TRP
239
A
GLU
254
A
GLU
248
A
LEU
238
A
LEU
232
A
PRO
239
A
PRO
233
A
GLN
227
A
GLN
221
A
GLU
228
A
GLU
222
A
TRP
219
A
TRP
213
A
ARG
224
A
ARG
218
A
LEU
261
A
LEU
255
A
LYS
266
A
LYS
260
A
ILE
275
A
ILE
269
A
TYR
278
A
TYR
272
B
GLN
6
B
GLN
6
B
SER
11
B
SER
11
B
ASN
21
B
ASN
21
B
PHE
30
B
PHE
30
B
PHE
62
B
PHE
62
B
PHE
70
B
PHE
70
B
GLU
50
B
GLU
50
B
MET
51
B
MET
51
B
GLN
6
B
GLN
6
B
SER
11
B
SER
11
B
ASN
21
B
ASN
21
B
PHE
30
B
PHE
30
B
PHE
62
B
PHE
62
B
PHE
70
B
PHE
70
B
SER
55
B
SER
55
B
PHE
56
B
PHE
56
B
LYS
44
B
LYS
44
B
LYS
45
B
LYS
45
B
GLU
36
B
GLU
36
B
LYS
41
B
LYS
41
B
TYR
78
B
TYR
78
B
LYS
83
B
LYS
83
B
LYS
91
B
LYS
91
B
TYR
94
B
TYR
94
19
orthorhombic
P 21 21 21