0.017926
0.000000
0.000000
-0.000000
0.013427
0.000000
0.000000
-0.000000
0.008136
0.000000
0.000000
0.000000
Wang, J.
Zajonc, D.M.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.000
90.000
90.000
55.785
74.479
122.917
C40 H79 N O9
718.057
N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexadecanamide
non-polymer
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C3 H7 N O2 S
121.158
y
CYSTEINE
L-peptide linking
C5 H10 N2 O3
146.144
y
GLUTAMINE
L-peptide linking
C5 H9 N O4
147.129
y
GLUTAMIC ACID
L-peptide linking
C2 H5 N O2
75.067
y
GLYCINE
peptide linking
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
C8 H15 N O6
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
N-acetyl-beta-D-glucosamine; 2-acetamido-2-deoxy-beta-D-glucose; 2-acetamido-2-deoxy-D-glucose; 2-acetamido-2-deoxy-glucose; N-ACETYL-D-GLUCOSAMINE
D-saccharide, beta linking
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
O4 S -2
96.063
SULFATE ION
non-polymer
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
C
N
2
N
C
N
3
N
C
N
4
N
C
N
5
N
C
N
6
N
C
N
7
N
C
N
8
N
C
N
9
N
C
N
10
N
C
N
11
N
C
N
12
N
C
N
13
N
C
N
14
N
C
N
15
R
C
N
16
N
O
N
17
S
C
N
18
N
O
N
19
S
C
N
20
N
C
N
21
N
O
N
22
S
C
N
23
N
O
N
24
R
C
N
25
N
C
N
26
N
O
N
27
R
C
N
28
N
O
N
29
S
C
N
30
N
O
N
31
R
C
N
32
N
O
N
33
N
N
N
34
N
C
N
35
N
O
N
36
N
C
N
37
N
C
N
38
N
C
N
39
N
C
N
40
N
C
N
41
N
C
N
42
N
C
N
43
N
C
N
44
N
C
N
45
N
C
N
46
N
C
N
47
N
C
N
48
N
C
N
49
N
C
N
50
N
C
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
H
N
64
N
H
N
65
N
H
N
66
N
H
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
H
N
75
N
H
N
76
N
H
N
77
N
H
N
78
N
H
N
79
N
H
N
80
N
H
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
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
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
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
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
H
N
121
N
H
N
122
N
H
N
123
N
H
N
124
N
H
N
125
N
H
N
126
N
H
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
N
N
131
S
C
N
132
N
C
N
133
N
O
N
134
N
C
N
135
N
O
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
N
N
144
S
C
N
145
N
C
N
146
N
O
N
147
N
C
N
148
N
C
N
149
N
C
N
150
N
N
N
151
N
C
N
152
N
N
N
153
N
N
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
H
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
H
N
169
N
H
N
170
N
N
N
171
S
C
N
172
N
C
N
173
N
O
N
174
N
C
N
175
N
C
N
176
N
O
N
177
N
N
N
178
N
O
N
179
N
H
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
N
N
188
S
C
N
189
N
C
N
190
N
O
N
191
N
C
N
192
N
C
N
193
N
O
N
194
N
O
N
195
N
O
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
N
N
204
R
C
N
205
N
C
N
206
N
O
N
207
N
C
N
208
N
S
N
209
N
O
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
N
N
218
S
C
N
219
N
C
N
220
N
O
N
221
N
C
N
222
N
C
N
223
N
C
N
224
N
O
N
225
N
N
N
226
N
O
N
227
N
H
N
228
N
H
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
N
N
238
S
C
N
239
N
C
N
240
N
O
N
241
N
C
N
242
N
C
N
243
N
C
N
244
N
O
N
245
N
O
N
246
N
O
N
247
N
H
N
248
N
H
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
N
N
257
N
C
N
258
N
C
N
259
N
O
N
260
N
O
N
261
N
H
N
262
N
H
N
263
N
H
N
264
N
H
N
265
N
H
N
266
N
N
N
267
S
C
N
268
N
C
N
269
N
O
N
270
N
C
Y
271
N
C
Y
272
N
N
Y
273
N
C
Y
274
N
C
Y
275
N
N
N
276
N
O
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
H
N
285
N
H
N
286
N
H
N
287
N
O
N
288
N
H
N
289
N
H
N
290
N
N
N
291
S
C
N
292
N
C
N
293
N
O
N
294
S
C
N
295
N
C
N
296
N
C
N
297
N
C
N
298
N
O
N
299
N
H
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
N
H
N
312
N
N
N
313
S
C
N
314
N
C
N
315
N
O
N
316
N
C
N
317
N
C
N
318
N
C
N
319
N
C
N
320
N
O
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
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
N
N
335
S
C
N
336
N
C
N
337
N
O
N
338
N
C
N
339
N
C
N
340
N
C
N
341
N
C
N
342
N
N
N
343
N
O
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
H
N
350
N
H
N
351
N
H
N
352
N
H
N
353
N
H
N
354
N
H
N
355
N
H
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
N
N
360
S
C
N
361
N
C
N
362
N
O
N
363
N
C
N
364
N
C
N
365
N
S
N
366
N
C
N
367
N
O
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
H
N
375
N
H
N
376
N
H
N
377
N
H
N
378
N
H
N
379
R
C
N
380
R
C
N
381
R
C
N
382
S
C
N
383
R
C
N
384
N
C
N
385
N
C
N
386
N
C
N
387
N
N
N
388
N
O
N
389
N
O
N
390
N
O
N
391
N
O
N
392
N
O
N
393
N
O
N
394
N
H
N
395
N
H
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
N
N
410
S
C
N
411
N
C
N
412
N
O
N
413
N
C
Y
414
N
C
Y
415
N
C
Y
416
N
C
Y
417
N
C
Y
418
N
C
Y
419
N
C
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
H
N
429
N
H
N
430
N
H
N
431
N
H
N
432
N
N
N
433
S
C
N
434
N
C
N
435
N
O
N
436
N
C
N
437
N
C
N
438
N
C
N
439
N
O
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
N
N
450
S
C
N
451
N
C
N
452
N
O
N
453
N
C
N
454
N
O
N
455
N
O
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
S
N
464
N
O
N
465
N
O
N
466
N
O
N
467
N
O
N
468
N
N
N
469
S
C
N
470
N
C
N
471
N
O
N
472
R
C
N
473
N
O
N
474
N
C
N
475
N
O
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
N
N
486
S
C
N
487
N
C
N
488
N
O
N
489
N
C
Y
490
N
C
Y
491
N
C
Y
492
N
C
Y
493
N
N
Y
494
N
C
Y
495
N
C
Y
496
N
C
Y
497
N
C
Y
498
N
C
N
499
N
O
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
H
N
510
N
H
N
511
N
H
N
512
N
N
N
513
S
C
N
514
N
C
N
515
N
O
N
516
N
C
Y
517
N
C
Y
518
N
C
Y
519
N
C
Y
520
N
C
Y
521
N
C
Y
522
N
C
N
523
N
O
N
524
N
O
N
525
N
H
N
526
N
H
N
527
N
H
N
528
N
H
N
529
N
H
N
530
N
H
N
531
N
H
N
532
N
H
N
533
N
H
N
534
N
H
N
535
N
H
N
536
N
N
N
537
S
C
N
538
N
C
N
539
N
O
N
540
N
C
N
541
N
C
N
542
N
C
N
543
N
O
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
H
N
554
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
sing
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
sing
N
20
N
sing
N
21
N
sing
N
22
N
doub
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
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
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
sing
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
sing
N
51
N
sing
N
52
N
sing
N
53
N
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
sing
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
sing
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
sing
N
77
N
sing
N
78
N
sing
N
79
N
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
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
doub
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
doub
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
doub
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
doub
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
doub
N
180
N
sing
N
181
N
sing
N
182
N
sing
N
183
N
sing
N
184
N
sing
N
185
N
sing
N
186
N
sing
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
doub
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
doub
N
206
N
sing
N
207
N
sing
N
208
N
sing
N
209
N
sing
N
210
N
sing
N
211
N
sing
N
212
N
sing
N
213
N
sing
N
214
N
sing
N
215
N
sing
N
216
N
sing
N
217
N
sing
N
218
N
doub
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
doub
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
doub
N
238
N
sing
N
239
N
sing
N
240
N
sing
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
doub
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
doub
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
doub
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
Y
269
N
sing
Y
270
N
doub
Y
271
N
doub
N
272
N
sing
Y
273
N
sing
N
274
N
sing
Y
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
doub
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
doub
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
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
doub
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
doub
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
doub
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
doub
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
Y
407
N
doub
Y
408
N
sing
Y
409
N
sing
N
410
N
sing
Y
411
N
doub
N
412
N
sing
Y
413
N
doub
N
414
N
sing
Y
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
doub
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
doub
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
doub
N
450
N
doub
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
doub
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
doub
N
476
N
sing
N
477
N
sing
N
478
N
sing
N
479
N
sing
Y
480
N
doub
Y
481
N
sing
Y
482
N
sing
N
483
N
sing
Y
484
N
doub
Y
485
N
sing
Y
486
N
sing
N
487
N
sing
Y
488
N
sing
Y
489
N
doub
N
490
N
sing
Y
491
N
doub
N
492
N
sing
Y
493
N
sing
N
494
N
sing
N
495
N
sing
N
496
N
sing
N
497
N
sing
N
498
N
sing
N
499
N
sing
N
500
N
sing
N
501
N
sing
N
502
N
sing
N
503
N
doub
N
504
N
sing
N
505
N
sing
N
506
N
sing
N
507
N
sing
Y
508
N
doub
Y
509
N
sing
Y
510
N
sing
N
511
N
sing
Y
512
N
doub
N
513
N
sing
Y
514
N
doub
N
515
N
sing
Y
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
doub
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
sing
US
Plos One
1932-6203
7
e47989
e47989
10.1371/journal.pone.0047989
23110152
Crystal Structures of Bovine CD1d Reveal Altered αGalCer Presentation and a Restricted A' Pocket Unable to Bind Long-Chain Glycolipids.
2012
10.2210/pdb4f7e/pdb
pdb_00004f7e
100
1
Rh coated flat mirror
PIXEL
2012-02-03
DECTRIS PILATUS 6M
Side scattering bent cube-root I-beam single crystal, asymmetric cut 4.965 degrees
SINGLE WAVELENGTH
M
x-ray
1
1.0
1.0
108859
0.059
1.57
2.150
40.000
28064
96.10
3.90
BL11-1
SSRL
1.0
SYNCHROTRON
SSRL BEAMLINE BL11-1
32460.561
CD1D antigen, d polypeptide
UNP residues 129-405
1
man
polymer
11653.148
Beta-2-microglobulin
UNP residues 21-118
1
man
polymer
424.401
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
1
man
branched
718.057
N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexadecanamide
1
syn
non-polymer
221.208
2-acetamido-2-deoxy-beta-D-glucopyranose
1
man
non-polymer
96.063
SULFATE ION
1
syn
non-polymer
18.015
water
26
nat
water
T cell surface glycoprotein CD1d antigen
Lactollin
no
no
SPAPQTPFSFQGLQISSFANRSWTRTDGLAWLGELQPYTWRNESDTIRFLKPWSRGTFSDQQWEQLQHTLLVYRSSFTRD
IWEFVEKLHVEYPLEIQIATGCELLPRNISESFLRAAFQGRDVLSFQGMSWVSAPDAPPFIQEVIKVLNQNQGTKETVHW
LLHDIWPELVRGVLQTGKSELEKQVKPEAWLSSGPSPGPGRLLLVCHVSGFYPKPVRVMWMRGEQEEPGTRQGDVMPNAD
STWYLRVTLDVAAGEVAGLSCQVKHSSLGDQDIILYWHHHHHH
SPAPQTPFSFQGLQISSFANRSWTRTDGLAWLGELQPYTWRNESDTIRFLKPWSRGTFSDQQWEQLQHTLLVYRSSFTRD
IWEFVEKLHVEYPLEIQIATGCELLPRNISESFLRAAFQGRDVLSFQGMSWVSAPDAPPFIQEVIKVLNQNQGTKETVHW
LLHDIWPELVRGVLQTGKSELEKQVKPEAWLSSGPSPGPGRLLLVCHVSGFYPKPVRVMWMRGEQEEPGTRQGDVMPNAD
STWYLRVTLDVAAGEVAGLSCQVKHSSLGDQDIILYWHHHHHH
A
polypeptide(L)
no
no
IQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDWSFYLLSHAEFTPNSKDQYSCR
VKHVTLEQPRIVKWDRDL
IQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDWSFYLLSHAEFTPNSKDQYSCR
VKHVTLEQPRIVKWDRDL
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
n
n
n
n
n
n
n
n
n
bovine
fall armyworm
sample
CD1D
9913
Bos taurus
7108
Spodoptera frugiperda
SF9
baculovirus
pBACpHp10
bovine
fall armyworm
sample
B2M
9913
Bos taurus
7108
Spodoptera frugiperda
SF9
baculovirus
pBACpHp10
1
2.90
57.54
VAPOR DIFFUSION, SITTING DROP
20% PEG4000, 200 mM potassium sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 295K
295
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_ref_seq_dif
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
Atomic model
Data collection
Database references
Derived calculations
Structure summary
Data collection
Database references
Refinement description
Structure summary
1
0
2012-11-14
2
0
2020-07-29
2
1
2023-09-13
_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_entity_nonpoly.entity_id
_pdbx_entity_nonpoly.name
_pdbx_struct_assembly_gen.asym_id_list
_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_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_ref_seq_dif.details
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
A
NAG
500
n
C
NAG
1
A
NAG
501
n
C
NAG
2
DGlcpNAcb
N-acetyl-b-D-glucopyranosamine
b-D-GlcpNAc
GlcNAc
Structure of a highly potent short-chain galactosyl ceramide agonist bound to CD1d
The crystal structure of human CD1d with and without alpha-Galactosylceramide
RCSB
Y
RCSB
2012-05-15
REL
REL
0.045
2.853
88.00
3.80
0.046
2.992
96.40
3.90
0.054
2.954
98.80
4.20
0.060
2.567
97.10
3.90
0.066
1.814
98.70
4.20
0.074
1.416
99.10
4.30
0.090
1.167
99.20
4.20
0.113
1.232
97.20
3.80
0.132
0.874
99.40
4.00
0.158
0.788
99.40
4.10
0.198
0.837
98.20
3.90
0.206
0.739
97.50
3.80
0.253
1.008
91.70
3.40
0.255
0.807
91.10
3.20
0.317
0.703
89.80
3.30
oligosaccharide
DGlcpNAcb1-4DGlcpNAcb1-
3
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1
3
PDB2Glycan
1.1.0
WURCS
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}
3
PDB-CARE
LINUCS
C1
O4
NAG
NAG
2
1
3
O1
HO4
sing
n
n
0SH
N-[(2S,3S,4R)-1-(alpha-D-galactopyranosyloxy)-3,4-dihydroxyoctadecan-2-yl]hexadecanamide
NAG
2-acetamido-2-deoxy-beta-D-glucopyranose
SO4
SULFATE ION
HOH
water
3L9R
PDB ENTRY 3L9R
PDB
experimental model
AGH
282
4
0SH
0SH
301
A
NAG
502
5
NAG
NAG
304
A
SO4
1
6
SO4
SO4
101
B
HOH
3
7
HOH
HOH
401
A
HOH
4
7
HOH
HOH
402
A
HOH
5
7
HOH
HOH
403
A
HOH
9
7
HOH
HOH
404
A
HOH
12
7
HOH
HOH
405
A
HOH
13
7
HOH
HOH
406
A
HOH
14
7
HOH
HOH
407
A
HOH
18
7
HOH
HOH
408
A
HOH
23
7
HOH
HOH
409
A
HOH
38
7
HOH
HOH
410
A
HOH
45
7
HOH
HOH
411
A
HOH
66
7
HOH
HOH
412
A
HOH
185
7
HOH
HOH
413
A
HOH
186
7
HOH
HOH
414
A
HOH
189
7
HOH
HOH
415
A
HOH
190
7
HOH
HOH
416
A
HOH
191
7
HOH
HOH
417
A
HOH
192
7
HOH
HOH
418
A
HOH
193
7
HOH
HOH
419
A
HOH
1
7
HOH
HOH
201
B
HOH
8
7
HOH
HOH
202
B
HOH
25
7
HOH
HOH
203
B
HOH
26
7
HOH
HOH
204
B
HOH
55
7
HOH
HOH
205
B
HOH
176
7
HOH
HOH
206
B
HOH
184
7
HOH
HOH
207
B
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
n
5
5
A
n
6
6
A
n
7
7
A
PHE
8
n
8
PHE
8
A
SER
9
n
9
SER
9
A
PHE
10
n
10
PHE
10
A
GLN
11
n
11
GLN
11
A
GLY
12
n
12
GLY
12
A
LEU
13
n
13
LEU
13
A
GLN
14
n
14
GLN
14
A
ILE
15
n
15
ILE
15
A
SER
16
n
16
SER
16
A
SER
17
n
17
SER
17
A
PHE
18
n
18
PHE
18
A
ALA
19
n
19
ALA
19
A
ASN
20
n
20
ASN
20
A
ARG
21
n
21
ARG
21
A
SER
22
n
22
SER
22
A
TRP
23
n
23
TRP
23
A
THR
24
n
24
THR
24
A
ARG
25
n
25
ARG
25
A
THR
26
n
26
THR
26
A
ASP
27
n
27
ASP
27
A
GLY
28
n
28
GLY
28
A
LEU
29
n
29
LEU
29
A
ALA
30
n
30
ALA
30
A
TRP
31
n
31
TRP
31
A
LEU
32
n
32
LEU
32
A
GLY
33
n
33
GLY
33
A
GLU
34
n
34
GLU
34
A
LEU
35
n
35
LEU
35
A
GLN
36
n
36
GLN
36
A
PRO
37
n
37
PRO
37
A
TYR
38
n
38
TYR
38
A
THR
39
n
39
THR
39
A
TRP
40
n
40
TRP
40
A
ARG
41
n
41
ARG
41
A
ASN
42
n
42
ASN
42
A
GLU
43
n
43
GLU
43
A
SER
44
n
44
SER
44
A
ASP
45
n
45
ASP
45
A
THR
46
n
46
THR
46
A
ILE
47
n
47
ILE
47
A
ARG
48
n
48
ARG
48
A
PHE
49
n
49
PHE
49
A
LEU
50
n
50
LEU
50
A
LYS
51
n
51
LYS
51
A
PRO
52
n
52
PRO
52
A
TRP
53
n
53
TRP
53
A
SER
54
n
54
SER
54
A
ARG
55
n
55
ARG
55
A
GLY
56
n
56
GLY
56
A
THR
57
n
57
THR
57
A
PHE
58
n
58
PHE
58
A
SER
59
n
59
SER
59
A
ASP
60
n
60
ASP
60
A
GLN
61
n
61
GLN
61
A
GLN
62
n
62
GLN
62
A
TRP
63
n
63
TRP
63
A
GLU
64
n
64
GLU
64
A
GLN
65
n
65
GLN
65
A
LEU
66
n
66
LEU
66
A
GLN
67
n
67
GLN
67
A
HIS
68
n
68
HIS
68
A
THR
69
n
69
THR
69
A
LEU
70
n
70
LEU
70
A
LEU
71
n
71
LEU
71
A
VAL
72
n
72
VAL
72
A
TYR
73
n
73
TYR
73
A
ARG
74
n
74
ARG
74
A
SER
75
n
75
SER
75
A
SER
76
n
76
SER
76
A
PHE
77
n
77
PHE
77
A
THR
78
n
78
THR
78
A
ARG
79
n
79
ARG
79
A
ASP
80
n
80
ASP
80
A
ILE
81
n
81
ILE
81
A
TRP
82
n
82
TRP
82
A
GLU
83
n
83
GLU
83
A
PHE
84
n
84
PHE
84
A
VAL
85
n
85
VAL
85
A
GLU
86
n
86
GLU
86
A
LYS
87
n
87
LYS
87
A
LEU
88
n
88
LEU
88
A
HIS
89
n
89
HIS
89
A
VAL
90
n
90
VAL
90
A
GLU
91
n
91
GLU
91
A
TYR
92
n
92
TYR
92
A
PRO
93
n
93
PRO
93
A
LEU
94
n
94
LEU
94
A
GLU
95
n
95
GLU
95
A
ILE
96
n
96
ILE
96
A
GLN
97
n
97
GLN
97
A
ILE
98
n
98
ILE
98
A
ALA
99
n
99
ALA
99
A
THR
100
n
100
THR
100
A
GLY
101
n
101
GLY
101
A
CYS
102
n
102
CYS
102
A
GLU
103
n
103
GLU
103
A
LEU
104
n
104
LEU
104
A
LEU
105
n
105
LEU
105
A
PRO
106
n
106
PRO
106
A
ARG
107
n
107
ARG
107
A
ASN
108
n
108
ASN
108
A
ILE
109
n
109
ILE
109
A
SER
110
n
110
SER
110
A
GLU
111
n
111
GLU
111
A
SER
112
n
112
SER
112
A
PHE
113
n
113
PHE
113
A
LEU
114
n
114
LEU
114
A
ARG
115
n
115
ARG
115
A
ALA
116
n
116
ALA
116
A
ALA
117
n
117
ALA
117
A
PHE
118
n
118
PHE
118
A
GLN
119
n
119
GLN
119
A
GLY
120
n
120
GLY
120
A
ARG
121
n
121
ARG
121
A
ASP
122
n
122
ASP
122
A
VAL
123
n
123
VAL
123
A
LEU
124
n
124
LEU
124
A
SER
125
n
125
SER
125
A
PHE
126
n
126
PHE
126
A
GLN
127
n
127
GLN
127
A
GLY
128
n
128
GLY
128
A
MET
129
n
129
MET
129
A
SER
130
n
130
SER
130
A
TRP
131
n
131
TRP
131
A
VAL
132
n
132
VAL
132
A
SER
133
n
133
SER
133
A
ALA
134
n
134
ALA
134
A
PRO
135
n
135
PRO
135
A
ASP
136
n
136
ASP
136
A
ALA
137
n
137
ALA
137
A
PRO
138
n
138
PRO
138
A
PRO
139
n
139
PRO
139
A
PHE
140
n
140
PHE
140
A
ILE
141
n
141
ILE
141
A
GLN
142
n
142
GLN
142
A
GLU
143
n
143
GLU
143
A
VAL
144
n
144
VAL
144
A
ILE
145
n
145
ILE
145
A
LYS
146
n
146
LYS
146
A
VAL
147
n
147
VAL
147
A
LEU
148
n
148
LEU
148
A
ASN
149
n
149
ASN
149
A
GLN
150
n
150
GLN
150
A
ASN
151
n
151
ASN
151
A
GLN
152
n
152
GLN
152
A
GLY
153
n
153
GLY
153
A
THR
154
n
154
THR
154
A
LYS
155
n
155
LYS
155
A
GLU
156
n
156
GLU
156
A
THR
157
n
157
THR
157
A
VAL
158
n
158
VAL
158
A
HIS
159
n
159
HIS
159
A
TRP
160
n
160
TRP
160
A
LEU
161
n
161
LEU
161
A
LEU
162
n
162
LEU
162
A
HIS
163
n
163
HIS
163
A
ASP
164
n
164
ASP
164
A
ILE
165
n
165
ILE
165
A
TRP
166
n
166
TRP
166
A
PRO
167
n
167
PRO
167
A
GLU
168
n
168
GLU
168
A
LEU
169
n
169
LEU
169
A
VAL
170
n
170
VAL
170
A
ARG
171
n
171
ARG
171
A
GLY
172
n
172
GLY
172
A
VAL
173
n
173
VAL
173
A
LEU
174
n
174
LEU
174
A
GLN
175
n
175
GLN
175
A
THR
176
n
176
THR
176
A
GLY
177
n
177
GLY
177
A
LYS
178
n
178
LYS
178
A
SER
179
n
179
SER
179
A
GLU
180
n
180
GLU
180
A
LEU
181
n
181
LEU
181
A
GLU
182
n
182
GLU
182
A
LYS
183
n
183
LYS
183
A
GLN
184
n
184
GLN
184
A
VAL
185
n
185
VAL
185
A
LYS
186
n
186
LYS
186
A
PRO
187
n
187
PRO
187
A
GLU
188
n
188
GLU
188
A
ALA
189
n
189
ALA
189
A
TRP
190
n
190
TRP
190
A
LEU
191
n
191
LEU
191
A
SER
192
n
192
SER
192
A
SER
193
n
193
SER
193
A
GLY
194
n
194
GLY
194
A
PRO
195
n
195
PRO
195
A
SER
196
n
196
SER
196
A
PRO
197
n
197
PRO
197
A
GLY
198
n
198
GLY
198
A
PRO
199
n
199
PRO
199
A
GLY
200
n
200
GLY
200
A
ARG
201
n
201
ARG
201
A
LEU
202
n
202
LEU
202
A
LEU
203
n
203
LEU
203
A
LEU
204
n
204
LEU
204
A
VAL
205
n
205
VAL
205
A
CYS
206
n
206
CYS
206
A
HIS
207
n
207
HIS
207
A
VAL
208
n
208
VAL
208
A
SER
209
n
209
SER
209
A
GLY
210
n
210
GLY
210
A
PHE
211
n
211
PHE
211
A
TYR
212
n
212
TYR
212
A
PRO
213
n
213
PRO
213
A
LYS
214
n
214
LYS
214
A
PRO
215
n
215
PRO
215
A
VAL
216
n
216
VAL
216
A
ARG
217
n
217
ARG
217
A
VAL
218
n
218
VAL
218
A
MET
219
n
219
MET
219
A
TRP
220
n
220
TRP
220
A
MET
221
n
221
MET
221
A
ARG
222
n
222
ARG
222
A
GLY
223
n
223
GLY
223
A
GLU
224
n
224
GLU
224
A
GLN
225
n
225
GLN
225
A
GLU
226
n
226
GLU
226
A
GLU
227
n
227
GLU
227
A
PRO
228
n
228
PRO
228
A
GLY
229
n
229
GLY
229
A
THR
230
n
230
THR
230
A
ARG
231
n
231
ARG
231
A
GLN
232
n
232
GLN
232
A
GLY
233
n
233
GLY
233
A
ASP
234
n
234
ASP
234
A
VAL
235
n
235
VAL
235
A
MET
236
n
236
MET
236
A
PRO
237
n
237
PRO
237
A
ASN
238
n
238
ASN
238
A
ALA
239
n
239
ALA
239
A
ASP
240
n
240
ASP
240
A
SER
241
n
241
SER
241
A
THR
242
n
242
THR
242
A
TRP
243
n
243
TRP
243
A
TYR
244
n
244
TYR
244
A
LEU
245
n
245
LEU
245
A
ARG
246
n
246
ARG
246
A
VAL
247
n
247
VAL
247
A
THR
248
n
248
THR
248
A
LEU
249
n
249
LEU
249
A
ASP
250
n
250
ASP
250
A
VAL
251
n
251
VAL
251
A
ALA
252
n
252
ALA
252
A
ALA
253
n
253
ALA
253
A
GLY
254
n
254
GLY
254
A
GLU
255
n
255
GLU
255
A
VAL
256
n
256
VAL
256
A
ALA
257
n
257
ALA
257
A
GLY
258
n
258
GLY
258
A
LEU
259
n
259
LEU
259
A
SER
260
n
260
SER
260
A
CYS
261
n
261
CYS
261
A
GLN
262
n
262
GLN
262
A
VAL
263
n
263
VAL
263
A
LYS
264
n
264
LYS
264
A
HIS
265
n
265
HIS
265
A
SER
266
n
266
SER
266
A
SER
267
n
267
SER
267
A
LEU
268
n
268
LEU
268
A
GLY
269
n
269
GLY
269
A
ASP
270
n
270
ASP
270
A
GLN
271
n
271
GLN
271
A
ASP
272
n
272
ASP
272
A
ILE
273
n
273
ILE
273
A
ILE
274
n
274
ILE
274
A
LEU
275
n
275
LEU
275
A
TYR
276
n
276
TYR
276
A
TRP
277
n
277
TRP
277
A
HIS
278
n
278
HIS
278
A
n
279
279
A
n
280
280
A
n
281
281
A
n
282
282
A
n
283
283
A
ILE
1
n
1
ILE
1
B
GLN
2
n
2
GLN
2
B
ARG
3
n
3
ARG
3
B
PRO
4
n
4
PRO
4
B
PRO
5
n
5
PRO
5
B
LYS
6
n
6
LYS
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
ASP
17
n
17
ASP
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
TYR
22
n
22
TYR
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
TYR
28
n
28
TYR
28
B
GLY
29
n
29
GLY
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
GLN
34
n
34
GLN
34
B
ILE
35
n
35
ILE
35
B
GLU
36
n
36
GLU
36
B
ILE
37
n
37
ILE
37
B
ASP
38
n
38
ASP
38
B
LEU
39
n
39
LEU
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
GLU
44
n
44
GLU
44
B
LYS
45
n
45
LYS
45
B
ILE
46
n
46
ILE
46
B
LYS
47
n
47
LYS
47
B
SER
48
n
48
SER
48
B
GLU
49
n
49
GLU
49
B
GLN
50
n
50
GLN
50
B
SER
51
n
51
SER
51
B
ASP
52
n
52
ASP
52
B
LEU
53
n
53
LEU
53
B
SER
54
n
54
SER
54
B
PHE
55
n
55
PHE
55
B
SER
56
n
56
SER
56
B
LYS
57
n
57
LYS
57
B
ASP
58
n
58
ASP
58
B
TRP
59
n
59
TRP
59
B
SER
60
n
60
SER
60
B
PHE
61
n
61
PHE
61
B
TYR
62
n
62
TYR
62
B
LEU
63
n
63
LEU
63
B
LEU
64
n
64
LEU
64
B
SER
65
n
65
SER
65
B
HIS
66
n
66
HIS
66
B
ALA
67
n
67
ALA
67
B
GLU
68
n
68
GLU
68
B
PHE
69
n
69
PHE
69
B
THR
70
n
70
THR
70
B
PRO
71
n
71
PRO
71
B
ASN
72
n
72
ASN
72
B
SER
73
n
73
SER
73
B
LYS
74
n
74
LYS
74
B
ASP
75
n
75
ASP
75
B
GLN
76
n
76
GLN
76
B
TYR
77
n
77
TYR
77
B
SER
78
n
78
SER
78
B
CYS
79
n
79
CYS
79
B
ARG
80
n
80
ARG
80
B
VAL
81
n
81
VAL
81
B
LYS
82
n
82
LYS
82
B
HIS
83
n
83
HIS
83
B
VAL
84
n
84
VAL
84
B
THR
85
n
85
THR
85
B
LEU
86
n
86
LEU
86
B
GLU
87
n
87
GLU
87
B
GLN
88
n
88
GLN
88
B
PRO
89
n
89
PRO
89
B
ARG
90
n
90
ARG
90
B
ILE
91
n
91
ILE
91
B
VAL
92
n
92
VAL
92
B
LYS
93
n
93
LYS
93
B
TRP
94
n
94
TRP
94
B
ASP
95
n
95
ASP
95
B
ARG
96
n
96
ARG
96
B
ASP
97
n
97
ASP
97
B
LEU
98
n
98
LEU
98
B
author_and_software_defined_assembly
PISA
2
dimeric
3760
-18
18570
A
ASN
20
GLYCOSYLATION SITE
A
ASN
20
ASN
A
ASN
42
GLYCOSYLATION SITE
A
ASN
42
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
ARG
48
A
O
ARG
48
A
N
THR
39
A
N
THR
39
A
O
TRP
40
A
O
TRP
40
A
N
GLY
28
A
N
GLY
28
A
O
ASP
27
A
O
ASP
27
A
N
ILE
15
A
N
ILE
15
A
N
GLY
12
A
N
GLY
12
A
O
THR
100
A
O
THR
100
A
N
GLN
97
A
N
GLN
97
A
O
ALA
117
A
O
ALA
117
A
N
ALA
116
A
N
ALA
116
A
O
LEU
124
A
O
LEU
124
A
N
GLN
127
A
N
GLN
127
A
O
SER
130
A
O
SER
130
A
N
TRP
190
A
N
TRP
190
A
O
HIS
207
A
O
HIS
207
A
N
GLY
210
A
N
GLY
210
A
O
TRP
243
A
O
TRP
243
A
O
THR
248
A
O
THR
248
A
N
ARG
231
A
N
ARG
231
A
N
TRP
190
A
N
TRP
190
A
O
HIS
207
A
O
HIS
207
A
N
GLY
210
A
N
GLY
210
A
O
TRP
243
A
O
TRP
243
A
O
TYR
244
A
O
TYR
244
A
N
MET
236
A
N
MET
236
A
O
GLN
225
A
O
GLN
225
A
N
ARG
222
A
N
ARG
222
A
N
ARG
217
A
N
ARG
217
A
O
LYS
264
A
O
LYS
264
A
N
VAL
263
A
N
VAL
263
A
O
ILE
273
A
O
ILE
273
B
N
GLN
8
B
N
GLN
8
B
O
TYR
26
B
O
TYR
26
B
N
LEU
23
B
N
LEU
23
B
O
ALA
67
B
O
ALA
67
B
O
HIS
66
B
O
HIS
66
B
N
GLU
49
B
N
GLU
49
B
N
GLN
8
B
N
GLN
8
B
O
TYR
26
B
O
TYR
26
B
N
LEU
23
B
N
LEU
23
B
O
ALA
67
B
O
ALA
67
B
O
TYR
62
B
O
TYR
62
B
N
SER
54
B
N
SER
54
B
O
GLU
44
B
O
GLU
44
B
N
LYS
41
B
N
LYS
41
B
N
ASP
38
B
N
ASP
38
B
O
ARG
80
B
O
ARG
80
B
N
VAL
81
B
N
VAL
81
B
O
ARG
90
B
O
ARG
90
1
A
CG
GLU
86
A
CG
GLU
86
1
Y
1
A
CD
GLU
86
A
CD
GLU
86
1
Y
1
A
OE1
GLU
86
A
OE1
GLU
86
1
Y
1
A
OE2
GLU
86
A
OE2
GLU
86
1
Y
1
A
CG
LYS
87
A
CG
LYS
87
1
Y
1
A
CD
LYS
87
A
CD
LYS
87
1
Y
1
A
CE
LYS
87
A
CE
LYS
87
1
Y
1
A
NZ
LYS
87
A
NZ
LYS
87
1
Y
1
A
CG
ARG
107
A
CG
ARG
107
1
Y
1
A
CD
ARG
107
A
CD
ARG
107
1
Y
1
A
NE
ARG
107
A
NE
ARG
107
1
Y
1
A
CZ
ARG
107
A
CZ
ARG
107
1
Y
1
A
NH1
ARG
107
A
NH1
ARG
107
1
Y
1
A
NH2
ARG
107
A
NH2
ARG
107
1
Y
1
A
CG1
ILE
109
A
CG1
ILE
109
1
Y
1
A
CG2
ILE
109
A
CG2
ILE
109
1
Y
1
A
CD1
ILE
109
A
CD1
ILE
109
1
Y
1
A
CG
ASP
136
A
CG
ASP
136
1
Y
1
A
OD1
ASP
136
A
OD1
ASP
136
1
Y
1
A
OD2
ASP
136
A
OD2
ASP
136
1
Y
1
A
CG
GLN
142
A
CG
GLN
142
1
Y
1
A
CD
GLN
142
A
CD
GLN
142
1
Y
1
A
OE1
GLN
142
A
OE1
GLN
142
1
Y
1
A
NE2
GLN
142
A
NE2
GLN
142
1
Y
1
A
CG
LYS
146
A
CG
LYS
146
1
Y
1
A
CD
LYS
146
A
CD
LYS
146
1
Y
1
A
CE
LYS
146
A
CE
LYS
146
1
Y
1
A
NZ
LYS
146
A
NZ
LYS
146
1
Y
1
A
CG
ARG
171
A
CG
ARG
171
1
Y
1
A
CD
ARG
171
A
CD
ARG
171
1
Y
1
A
NE
ARG
171
A
NE
ARG
171
1
Y
1
A
CZ
ARG
171
A
CZ
ARG
171
1
Y
1
A
NH1
ARG
171
A
NH1
ARG
171
1
Y
1
A
NH2
ARG
171
A
NH2
ARG
171
1
Y
1
A
CG
GLU
224
A
CG
GLU
224
1
Y
1
A
CD
GLU
224
A
CD
GLU
224
1
Y
1
A
OE1
GLU
224
A
OE1
GLU
224
1
Y
1
A
OE2
GLU
224
A
OE2
GLU
224
1
Y
1
A
CG
GLN
225
A
CG
GLN
225
1
Y
1
A
CD
GLN
225
A
CD
GLN
225
1
Y
1
A
OE1
GLN
225
A
OE1
GLN
225
1
Y
1
A
NE2
GLN
225
A
NE2
GLN
225
1
Y
1
A
CG
ASP
270
A
CG
ASP
270
1
Y
1
A
OD1
ASP
270
A
OD1
ASP
270
1
Y
1
A
OD2
ASP
270
A
OD2
ASP
270
1
Y
1
B
CG
LYS
19
B
CG
LYS
19
1
Y
1
B
CD
LYS
19
B
CD
LYS
19
1
Y
1
B
CE
LYS
19
B
CE
LYS
19
1
Y
1
B
NZ
LYS
19
B
NZ
LYS
19
1
Y
1
B
CG
GLU
44
B
CG
GLU
44
1
Y
1
B
CD
GLU
44
B
CD
GLU
44
1
Y
1
B
OE1
GLU
44
B
OE1
GLU
44
1
Y
1
B
OE2
GLU
44
B
OE2
GLU
44
1
Y
1
B
CG
LYS
45
B
CG
LYS
45
1
Y
1
B
CD
LYS
45
B
CD
LYS
45
1
Y
1
B
CE
LYS
45
B
CE
LYS
45
1
Y
1
B
NZ
LYS
45
B
NZ
LYS
45
1
Y
1
B
CG
LYS
57
B
CG
LYS
57
1
Y
1
B
CD
LYS
57
B
CD
LYS
57
1
Y
1
B
CE
LYS
57
B
CE
LYS
57
1
Y
1
B
NZ
LYS
57
B
NZ
LYS
57
1
Y
1
B
CG
LYS
74
B
CG
LYS
74
1
Y
1
B
CD
LYS
74
B
CD
LYS
74
1
Y
1
B
CE
LYS
74
B
CE
LYS
74
1
Y
1
B
NZ
LYS
74
B
NZ
LYS
74
1
Y
1
B
CG
LYS
82
B
CG
LYS
82
1
Y
1
B
CD
LYS
82
B
CD
LYS
82
1
Y
1
B
CE
LYS
82
B
CE
LYS
82
1
Y
1
B
NZ
LYS
82
B
NZ
LYS
82
1
Y
1
B
CG
GLU
87
B
CG
GLU
87
1
Y
1
B
CD
GLU
87
B
CD
GLU
87
1
Y
1
B
OE1
GLU
87
B
OE1
GLU
87
1
Y
1
B
OE2
GLU
87
B
OE2
GLU
87
1
Y
1
A
SER
1
A
SER
1
1
Y
1
A
PRO
2
A
PRO
2
1
Y
1
A
ALA
3
A
ALA
3
1
Y
1
A
PRO
4
A
PRO
4
1
Y
1
A
GLN
5
A
GLN
5
1
Y
1
A
THR
6
A
THR
6
1
Y
1
A
PRO
7
A
PRO
7
1
Y
1
A
HIS
279
A
HIS
279
1
Y
1
A
HIS
280
A
HIS
280
1
Y
1
A
HIS
281
A
HIS
281
1
Y
1
A
HIS
282
A
HIS
282
1
Y
1
A
HIS
283
A
HIS
283
1
Y
1
A
ASN
20
-114.62
-129.43
1
A
LEU
88
-150.04
11.77
1
A
GLU
91
-63.38
-179.93
1
A
PRO
106
-54.16
171.01
1
A
ARG
107
63.95
-100.83
1
A
VAL
123
-138.07
-40.64
1
A
MET
129
-140.28
-6.09
1
A
PRO
138
-43.22
150.59
1
B
HIS
31
176.70
125.33
1
B
TRP
59
79.80
-0.62
132.440
61.7012
30.290
0.0700
-0.0000
-0.0000
-0.0500
0.0000
-0.0300
0.9490
0.9180
HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
U VALUES : REFINED INDIVIDUALLY
0.2763
0.2211
0.2233
0.2233
2.400
35.9
804
20132
4.0
97.31
0.2878
0.2328
1.000
1.000
0.7586
9.7390
0.2180
0.3582
0.2704
RANDOM
1
THROUGHOUT
0.0
MOLECULAR REPLACEMENT
0.3580
0.2700
0.8000
0.8000
1.2000
PDB ENTRY 3L9R
MAXIMUM LIKELIHOOD
MASK
2.400
35.9
26
3070
97
0
2947
0.011
0.022
3140
1.400
1.965
4282
6.161
5.000
367
35.365
23.611
144
16.911
15.000
466
21.572
15.000
19
0.088
0.200
462
0.007
0.021
2401
0.3900
0.4010
2.462
55
1277
1332
1332
20
98.52
45.6
2.4
40
4F7E
20240
20240
0
0
0.067
1
35
4.1
97.4
0.199
2.4
2.46
4.9
1901
1
4.1
98.2
phasing
Randy J. Read
cimr-phaser@lists.cam.ac.uk
http://www-structmed.cimr.cam.ac.uk/phaser/
PHASER
program
refinement
Garib N. Murshudov
garib@ysbl.york.ac.uk
Fortran_77
http://www.ccp4.ac.uk/dist/html/refmac5.html
REFMAC
program
data extraction
PDB
deposit@deposit.rcsb.org
April 22, 2011
C++
http://sw-tools.pdb.org/apps/PDB_EXTRACT/
PDB_EXTRACT
package
3.11
data collection
HKL-2000
data reduction
HKL-2000
data scaling
HKL-2000
Crystal structure of bovine CD1d with bound C16:0-alpha-galactosyl ceramide
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
6
N
N
7
N
N
7
N
N
A
SER
59
A
SER
59
HELX_P
A
LYS
87
A
LYS
87
1
1
29
A
PHE
140
A
PHE
140
HELX_P
A
ASN
149
A
ASN
149
1
2
10
A
ASN
151
A
ASN
151
HELX_P
A
ASP
164
A
ASP
164
1
3
14
A
ASP
164
A
ASP
164
HELX_P
A
GLY
177
A
GLY
177
1
4
14
A
GLY
177
A
GLY
177
HELX_P
A
GLU
182
A
GLU
182
1
5
6
A
GLY
254
A
GLY
254
HELX_P
A
ALA
257
A
ALA
257
5
6
4
disulf
2.050
A
CYS
206
A
SG
CYS
206
1_555
A
CYS
261
A
SG
CYS
261
1_555
disulf
2.058
B
CYS
25
B
SG
CYS
25
1_555
B
CYS
79
B
SG
CYS
79
1_555
covale
1.447
one
N-Glycosylation
A
ASN
20
A
ND2
ASN
20
1_555
C
NAG
1
C
C1
NAG
1_555
covale
1.449
one
N-Glycosylation
A
ASN
42
A
ND2
ASN
42
1_555
A
NAG
304
E
C1
NAG
1_555
covale
1.448
both
C
NAG
1
C
O4
NAG
1_555
C
NAG
2
C
C1
NAG
1_555
IMMUNE SYSTEM
protein-glycolipid complex, MHC-fold, Ig-fold, antigen presentation, TCR, membrane, IMMUNE SYSTEM
A
TYR
92
A
TYR
92
1
A
PRO
93
A
PRO
93
-10.36
A
TYR
212
A
TYR
212
1
A
PRO
213
A
PRO
213
-5.26
B
HIS
31
B
HIS
31
1
B
PRO
32
B
PRO
32
5.50
A1L565_BOVIN
UNP
1
129
A1L565
SPAPQTPFSFQGLQISSFANRSWTRTDGLAWLGELQPYTWRNESDTIRFLKPWSRGTFSDQQWEQLQHTLLVYRSSFTRD
IWEFVEKLHVEYPLEIQIATGCELLPRNISESFLRAAFQGRDVLSFQGMSWVSAPDAPPFIQEVIKVLNQNQGTKETVHW
LLHDIWPELVRGVLQTGKSELEKQVKPEAWLSSGPSPGPGRLLLVCHVSGFYPKPVRVMWMRGEQEEPGTRQGDVMPNAD
STWYLRVTLDVAAGEVAGLSCQVKHSSLGDQDIILYW
B2MG_BOVIN
UNP
2
21
P01888
IQRPPKIQVYSRHPPEDGKPNYLNCYVYGFHPPQIEIDLLKNGEKIKSEQSDLSFSKDWSFYLLSHAEFTPNSKDQYSCR
VKHVTLEQPRIVKWDRDL
129
405
4F7E
1
277
A1L565
A
1
1
277
21
118
4F7E
1
98
P01888
B
2
1
98
1
expression tag
HIS
278
4F7E
A
A1L565
UNP
278
1
expression tag
HIS
279
4F7E
A
A1L565
UNP
279
1
expression tag
HIS
280
4F7E
A
A1L565
UNP
280
1
expression tag
HIS
281
4F7E
A
A1L565
UNP
281
1
expression tag
HIS
282
4F7E
A
A1L565
UNP
282
1
expression tag
HIS
283
4F7E
A
A1L565
UNP
283
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
ARG
48
A
ARG
48
A
PHE
49
A
PHE
49
A
LEU
35
A
LEU
35
A
TRP
40
A
TRP
40
A
THR
24
A
THR
24
A
LEU
32
A
LEU
32
A
PHE
10
A
PHE
10
A
PHE
18
A
PHE
18
A
LEU
94
A
LEU
94
A
LEU
104
A
LEU
104
A
SER
110
A
SER
110
A
PHE
118
A
PHE
118
A
ARG
121
A
ARG
121
A
GLN
127
A
GLN
127
A
SER
130
A
SER
130
A
SER
133
A
SER
133
A
GLU
188
A
GLU
188
A
SER
193
A
SER
193
A
ARG
201
A
ARG
201
A
PHE
211
A
PHE
211
A
TRP
243
A
TRP
243
A
ALA
252
A
ALA
252
A
ARG
231
A
ARG
231
A
GLN
232
A
GLN
232
A
GLU
188
A
GLU
188
A
SER
193
A
SER
193
A
ARG
201
A
ARG
201
A
PHE
211
A
PHE
211
A
TRP
243
A
TRP
243
A
ALA
252
A
ALA
252
A
MET
236
A
MET
236
A
PRO
237
A
PRO
237
A
GLN
225
A
GLN
225
A
GLU
226
A
GLU
226
A
VAL
216
A
VAL
216
A
ARG
222
A
ARG
222
A
LEU
259
A
LEU
259
A
HIS
265
A
HIS
265
A
ILE
273
A
ILE
273
A
TYR
276
A
TYR
276
B
LYS
6
B
LYS
6
B
SER
11
B
SER
11
B
ASN
21
B
ASN
21
B
PHE
30
B
PHE
30
B
PHE
61
B
PHE
61
B
PHE
69
B
PHE
69
B
GLU
49
B
GLU
49
B
GLN
50
B
GLN
50
B
LYS
6
B
LYS
6
B
SER
11
B
SER
11
B
ASN
21
B
ASN
21
B
PHE
30
B
PHE
30
B
PHE
61
B
PHE
61
B
PHE
69
B
PHE
69
B
SER
54
B
SER
54
B
PHE
55
B
PHE
55
B
GLU
44
B
GLU
44
B
LYS
45
B
LYS
45
B
GLU
36
B
GLU
36
B
LYS
41
B
LYS
41
B
TYR
77
B
TYR
77
B
LYS
82
B
LYS
82
B
ARG
90
B
ARG
90
B
LYS
93
B
LYS
93
19
P 21 21 21