0.009766
0.005638
0.000000
0.000000
0.011276
0.000000
0.000000
0.000000
0.008921
0.00000
0.00000
0.00000
Kouyama, T.
Okumura, H.
RIKEN Structural Genomics/Proteomics Initiative (RSGI)
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
12
90.00
90.00
120.00
102.400
102.400
112.100
C3 H7 N O2
89.093
y
ALANINE
L-peptide linking
C6 H15 N4 O2 1
175.209
y
ARGININE
L-peptide linking
C4 H8 N2 O3
132.118
y
ASPARAGINE
L-peptide linking
C4 H7 N O4
133.103
y
ASPARTIC ACID
L-peptide linking
C6 H12 O6
180.156
beta-D-galactopyranose
beta-D-galactose; D-galactose; galactose
D-saccharide, beta linking
C6 H12 O6
180.156
alpha-D-glucopyranose
alpha-D-glucose; D-glucose; glucose
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
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C43 H88 O3
653.157
2,3-DI-PHYTANYL-GLYCEROL
1,2-DI-1-(3,7,11,15-TETRAMETHYL-HEXADECANE)-SN-GLYCEROL
non-polymer
C46 H94 O11 P2 -2
885.179
2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
non-polymer
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
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
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C20 H28 O
284.436
RETINAL
non-polymer
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
R
C
N
75
R
C
N
76
S
C
N
77
R
C
N
78
R
C
N
79
N
C
N
80
N
O
N
81
N
O
N
82
N
O
N
83
N
O
N
84
N
O
N
85
N
O
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
S
C
N
99
R
C
N
100
S
C
N
101
S
C
N
102
R
C
N
103
N
C
N
104
N
O
N
105
N
O
N
106
N
O
N
107
N
O
N
108
N
O
N
109
N
O
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
N
N
123
S
C
N
124
N
C
N
125
N
O
N
126
N
C
N
127
N
C
N
128
N
C
N
129
N
O
N
130
N
N
N
131
N
O
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
H
N
138
N
H
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
N
N
143
S
C
N
144
N
C
N
145
N
O
N
146
N
C
N
147
N
C
N
148
N
C
N
149
N
O
N
150
N
O
N
151
N
O
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
N
H
N
159
N
H
N
160
N
H
N
161
N
N
N
162
N
C
N
163
N
C
N
164
N
O
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
O
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
S
C
N
179
N
C
N
180
N
C
N
181
N
C
N
182
N
O
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
C
N
197
N
O
N
198
R
C
N
199
N
O
N
200
N
C
N
201
N
O
N
202
N
C
N
203
N
C
N
204
R
C
N
205
N
C
N
206
N
C
N
207
N
C
N
208
N
C
N
209
R
C
N
210
N
C
N
211
N
C
N
212
N
C
N
213
N
C
N
214
R
C
N
215
N
C
N
216
N
C
N
217
N
C
N
218
N
C
N
219
N
C
N
220
N
C
N
221
N
C
N
222
N
C
N
223
N
C
N
224
R
C
N
225
N
C
N
226
N
C
N
227
N
C
N
228
N
C
N
229
R
C
N
230
N
C
N
231
N
C
N
232
N
C
N
233
N
C
N
234
R
C
N
235
N
C
N
236
N
C
N
237
N
C
N
238
N
C
N
239
N
C
N
240
N
C
N
241
N
C
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
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
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
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
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
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
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
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
C
N
331
S
C
N
332
N
C
N
333
N
C
N
334
R
C
N
335
N
C
N
336
N
O
N
337
N
O
N
338
N
O
N
339
N
O
N
340
N
O
N
341
N
O
N
342
N
O
N
343
N
O
N
344
N
O
N
345
N
O
N
346
N
O
N
347
N
P
N
348
N
P
N
349
N
C
N
350
N
C
N
351
R
C
N
352
N
C
N
353
N
C
N
354
N
C
N
355
N
C
N
356
R
C
N
357
N
C
N
358
N
C
N
359
N
C
N
360
N
C
N
361
R
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
C
N
370
N
C
N
371
R
C
N
372
N
C
N
373
N
C
N
374
N
C
N
375
N
C
N
376
R
C
N
377
N
C
N
378
N
C
N
379
N
C
N
380
N
C
N
381
R
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
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
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
N
N
484
S
C
N
485
N
C
N
486
N
O
N
487
N
C
N
488
N
C
N
489
N
C
N
490
N
C
N
491
N
O
N
492
N
H
N
493
N
H
N
494
N
H
N
495
N
H
N
496
N
H
N
497
N
H
N
498
N
H
N
499
N
H
N
500
N
H
N
501
N
H
N
502
N
H
N
503
N
H
N
504
N
H
N
505
N
N
N
506
S
C
N
507
N
C
N
508
N
O
N
509
N
C
N
510
N
C
N
511
N
C
N
512
N
C
N
513
N
N
N
514
N
O
N
515
N
H
N
516
N
H
N
517
N
H
N
518
N
H
N
519
N
H
N
520
N
H
N
521
N
H
N
522
N
H
N
523
N
H
N
524
N
H
N
525
N
H
N
526
N
H
N
527
N
H
N
528
N
H
N
529
N
H
N
530
S
C
N
531
S
C
N
532
S
C
N
533
S
C
N
534
R
C
N
535
N
C
N
536
N
O
N
537
N
O
N
538
N
O
N
539
N
O
N
540
N
O
N
541
N
O
N
542
N
H
N
543
N
H
N
544
N
H
N
545
N
H
N
546
N
H
N
547
N
H
N
548
N
H
N
549
N
H
N
550
N
H
N
551
N
H
N
552
N
H
N
553
N
H
N
554
N
N
N
555
S
C
N
556
N
C
N
557
N
O
N
558
N
C
N
559
N
C
N
560
N
S
N
561
N
C
N
562
N
O
N
563
N
H
N
564
N
H
N
565
N
H
N
566
N
H
N
567
N
H
N
568
N
H
N
569
N
H
N
570
N
H
N
571
N
H
N
572
N
H
N
573
N
H
N
574
N
N
N
575
S
C
N
576
N
C
N
577
N
O
N
578
N
C
Y
579
N
C
Y
580
N
C
Y
581
N
C
Y
582
N
C
Y
583
N
C
Y
584
N
C
N
585
N
O
N
586
N
H
N
587
N
H
N
588
N
H
N
589
N
H
N
590
N
H
N
591
N
H
N
592
N
H
N
593
N
H
N
594
N
H
N
595
N
H
N
596
N
H
N
597
N
N
N
598
S
C
N
599
N
C
N
600
N
O
N
601
N
C
N
602
N
C
N
603
N
C
N
604
N
O
N
605
N
H
N
606
N
H
N
607
N
H
N
608
N
H
N
609
N
H
N
610
N
H
N
611
N
H
N
612
N
H
N
613
N
H
N
614
N
C
N
615
N
C
N
616
N
C
N
617
N
C
N
618
N
C
N
619
N
C
N
620
N
C
N
621
N
C
N
622
N
C
N
623
N
C
N
624
N
C
N
625
N
C
N
626
N
C
N
627
N
C
N
628
N
C
N
629
N
O
N
630
N
C
N
631
N
C
N
632
N
C
N
633
N
C
N
634
N
C
N
635
N
H
N
636
N
H
N
637
N
H
N
638
N
H
N
639
N
H
N
640
N
H
N
641
N
H
N
642
N
H
N
643
N
H
N
644
N
H
N
645
N
H
N
646
N
H
N
647
N
H
N
648
N
H
N
649
N
H
N
650
N
H
N
651
N
H
N
652
N
H
N
653
N
H
N
654
N
H
N
655
N
H
N
656
N
H
N
657
N
H
N
658
N
H
N
659
N
H
N
660
N
H
N
661
N
H
N
662
N
H
N
663
N
N
N
664
S
C
N
665
N
C
N
666
N
O
N
667
N
C
N
668
N
O
N
669
N
O
N
670
N
H
N
671
N
H
N
672
N
H
N
673
N
H
N
674
N
H
N
675
N
H
N
676
N
H
N
677
N
N
N
678
S
C
N
679
N
C
N
680
N
O
N
681
R
C
N
682
N
O
N
683
N
C
N
684
N
O
N
685
N
H
N
686
N
H
N
687
N
H
N
688
N
H
N
689
N
H
N
690
N
H
N
691
N
H
N
692
N
H
N
693
N
H
N
694
N
N
N
695
S
C
N
696
N
C
N
697
N
O
N
698
N
C
Y
699
N
C
Y
700
N
C
Y
701
N
C
Y
702
N
N
Y
703
N
C
Y
704
N
C
Y
705
N
C
Y
706
N
C
Y
707
N
C
N
708
N
O
N
709
N
H
N
710
N
H
N
711
N
H
N
712
N
H
N
713
N
H
N
714
N
H
N
715
N
H
N
716
N
H
N
717
N
H
N
718
N
H
N
719
N
H
N
720
N
H
N
721
N
N
N
722
S
C
N
723
N
C
N
724
N
O
N
725
N
C
Y
726
N
C
Y
727
N
C
Y
728
N
C
Y
729
N
C
Y
730
N
C
Y
731
N
C
N
732
N
O
N
733
N
O
N
734
N
H
N
735
N
H
N
736
N
H
N
737
N
H
N
738
N
H
N
739
N
H
N
740
N
H
N
741
N
H
N
742
N
H
N
743
N
H
N
744
N
H
N
745
N
N
N
746
S
C
N
747
N
C
N
748
N
O
N
749
N
C
N
750
N
C
N
751
N
C
N
752
N
O
N
753
N
H
N
754
N
H
N
755
N
H
N
756
N
H
N
757
N
H
N
758
N
H
N
759
N
H
N
760
N
H
N
761
N
H
N
762
N
H
N
763
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
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
doub
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
doub
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
doub
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
doub
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
doub
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
doub
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
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
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
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
sing
N
216
N
sing
N
217
N
sing
N
218
N
sing
N
219
N
sing
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
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
sing
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
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
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
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
doub
N
347
N
sing
N
348
N
doub
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
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
sing
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
N
379
N
sing
N
380
N
sing
N
381
N
sing
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
sing
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
N
409
N
sing
N
410
N
sing
N
411
N
sing
N
412
N
sing
N
413
N
sing
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
sing
N
478
N
doub
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
sing
N
488
N
sing
N
489
N
sing
N
490
N
sing
N
491
N
sing
N
492
N
sing
N
493
N
sing
N
494
N
sing
N
495
N
sing
N
496
N
sing
N
497
N
sing
N
498
N
sing
N
499
N
doub
N
500
N
sing
N
501
N
sing
N
502
N
sing
N
503
N
sing
N
504
N
sing
N
505
N
sing
N
506
N
sing
N
507
N
sing
N
508
N
sing
N
509
N
sing
N
510
N
sing
N
511
N
sing
N
512
N
sing
N
513
N
sing
N
514
N
sing
N
515
N
sing
N
516
N
sing
N
517
N
sing
N
518
N
sing
N
519
N
sing
N
520
N
sing
N
521
N
sing
N
522
N
sing
N
523
N
sing
N
524
N
sing
N
525
N
sing
N
526
N
sing
N
527
N
sing
N
528
N
sing
N
529
N
sing
N
530
N
sing
N
531
N
sing
N
532
N
sing
N
533
N
sing
N
534
N
sing
N
535
N
sing
N
536
N
sing
N
537
N
sing
N
538
N
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
sing
N
547
N
doub
N
548
N
sing
N
549
N
sing
N
550
N
sing
N
551
N
sing
N
552
N
sing
N
553
N
sing
N
554
N
sing
N
555
N
sing
N
556
N
sing
N
557
N
sing
N
558
N
sing
N
559
N
sing
N
560
N
sing
N
561
N
sing
N
562
N
sing
N
563
N
sing
N
564
N
sing
N
565
N
sing
N
566
N
doub
N
567
N
sing
N
568
N
sing
N
569
N
sing
N
570
N
sing
Y
571
N
doub
Y
572
N
sing
Y
573
N
sing
N
574
N
sing
Y
575
N
doub
N
576
N
sing
Y
577
N
doub
N
578
N
sing
Y
579
N
sing
N
580
N
sing
N
581
N
sing
N
582
N
sing
N
583
N
sing
N
584
N
sing
N
585
N
sing
N
586
N
sing
N
587
N
sing
N
588
N
sing
N
589
N
doub
N
590
N
sing
N
591
N
sing
N
592
N
sing
N
593
N
sing
N
594
N
sing
N
595
N
sing
N
596
N
sing
N
597
N
sing
N
598
N
sing
N
599
N
sing
N
600
N
sing
N
601
N
sing
N
602
N
sing
N
603
N
sing
N
604
N
sing
N
605
N
sing
N
606
N
sing
N
607
N
sing
N
608
N
sing
N
609
N
sing
N
610
N
sing
N
611
N
sing
N
612
N
sing
N
613
N
doub
N
614
N
sing
N
615
N
sing
N
616
E
doub
N
617
N
sing
N
618
N
sing
N
619
N
sing
N
620
E
doub
N
621
N
sing
N
622
N
sing
N
623
N
sing
N
624
E
doub
N
625
N
sing
N
626
N
sing
N
627
N
sing
N
628
E
doub
N
629
N
sing
N
630
N
sing
N
631
N
sing
N
632
N
doub
N
633
N
sing
N
634
N
sing
N
635
N
sing
N
636
N
sing
N
637
N
sing
N
638
N
sing
N
639
N
sing
N
640
N
sing
N
641
N
sing
N
642
N
sing
N
643
N
sing
N
644
N
sing
N
645
N
sing
N
646
N
sing
N
647
N
sing
N
648
N
sing
N
649
N
sing
N
650
N
sing
N
651
N
sing
N
652
N
sing
N
653
N
sing
N
654
N
sing
N
655
N
doub
N
656
N
sing
N
657
N
sing
N
658
N
sing
N
659
N
sing
N
660
N
sing
N
661
N
sing
N
662
N
sing
N
663
N
sing
N
664
N
sing
N
665
N
sing
N
666
N
sing
N
667
N
sing
N
668
N
doub
N
669
N
sing
N
670
N
sing
N
671
N
sing
N
672
N
sing
N
673
N
sing
N
674
N
sing
N
675
N
sing
N
676
N
sing
N
677
N
sing
N
678
N
sing
N
679
N
sing
N
680
N
sing
N
681
N
sing
N
682
N
sing
N
683
N
sing
N
684
N
doub
N
685
N
sing
N
686
N
sing
N
687
N
sing
N
688
N
sing
Y
689
N
doub
Y
690
N
sing
Y
691
N
sing
N
692
N
sing
Y
693
N
doub
Y
694
N
sing
Y
695
N
sing
N
696
N
sing
Y
697
N
sing
Y
698
N
doub
N
699
N
sing
Y
700
N
doub
N
701
N
sing
Y
702
N
sing
N
703
N
sing
N
704
N
sing
N
705
N
sing
N
706
N
sing
N
707
N
sing
N
708
N
sing
N
709
N
sing
N
710
N
sing
N
711
N
sing
N
712
N
doub
N
713
N
sing
N
714
N
sing
N
715
N
sing
N
716
N
sing
Y
717
N
doub
Y
718
N
sing
Y
719
N
sing
N
720
N
sing
Y
721
N
doub
N
722
N
sing
Y
723
N
doub
N
724
N
sing
Y
725
N
sing
N
726
N
sing
N
727
N
sing
N
728
N
sing
N
729
N
sing
N
730
N
sing
N
731
N
sing
N
732
N
sing
N
733
N
sing
N
734
N
sing
N
735
N
sing
N
736
N
doub
N
737
N
sing
N
738
N
sing
N
739
N
sing
N
740
N
sing
N
741
N
sing
N
742
N
sing
N
743
N
sing
N
744
N
sing
N
745
N
sing
N
746
N
sing
N
747
N
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
324
469
481
10.1016/S0022-2836(02)01110-5
12445782
Specific Damage Induced by X-ray Radiation and Structural Changes in the Primary
Photoreaction of Bacteriorhodopsin.
2002
10.2210/pdb1iw6/pdb
pdb_00001iw6
GLC B 1 HAS WRONG CHIRALITY AT ATOM C1
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
100.0
1
mirrors
CCD
2001-05-04
MARRESEARCH
Si 111 CHANNEL
SINGLE WAVELENGTH
M
x-ray
1
1.0
1.0
BL41XU
SPring-8
1.0
SYNCHROTRON
SPRING-8 BEAMLINE BL41XU
26814.412
bacteriorhodopsin
1
nat
polymer
504.438
beta-D-galactopyranose-(1-6)-alpha-D-mannopyranose-(1-2)-alpha-D-glucopyranose
1
man
branched
284.436
RETINAL
1
syn
non-polymer
885.179
2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
4
syn
non-polymer
653.157
2,3-DI-PHYTANYL-GLYCEROL
1
syn
non-polymer
18.015
water
41
nat
water
no
no
QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYW
ARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKA
ESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSA
GDGAAATS
QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYW
ARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKA
ESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSA
GDGAAATS
A
my_001000028.1
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
Halobacterium
sample
2242
Halobacterium salinarum
jw3
1
3.16
61.10
VAPOR DIFFUSION, SITTING DROP
5.2
ammonium sulfate, pH 5.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
293
RIKEN Structural Genomics/Proteomics Initiative
RSGI
chem_comp
reflns_shell
struct_conn
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_unobs_or_zero_occ_atoms
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
struct_conn
repository
Initial release
Carbohydrate remediation
repository
Remediation
Version format compliance
Version format compliance
Data collection
Derived calculations
Advisory
Atomic model
Data collection
Derived calculations
Structure summary
Data collection
Database references
Derived calculations
Refinement description
Structure summary
1
0
2002-12-11
1
1
2008-04-27
1
2
2011-07-13
1
3
2019-11-06
2
0
2020-07-29
2
1
2023-10-25
_chem_comp.type
_reflns_shell.Rmerge_I_obs
_reflns_shell.pdbx_Rsym_value
_struct_conn.pdbx_leaving_atom_flag
_atom_site.auth_asym_id
_atom_site.auth_seq_id
_atom_site.label_asym_id
_atom_site.label_entity_id
_chem_comp.name
_chem_comp.type
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_unobs_or_zero_occ_atoms.label_asym_id
_pdbx_validate_chiral.auth_asym_id
_pdbx_validate_chiral.auth_seq_id
_struct_conn.ptnr1_auth_asym_id
_struct_conn.ptnr1_auth_comp_id
_struct_conn.ptnr1_auth_seq_id
_struct_conn.ptnr1_label_asym_id
_struct_conn.ptnr1_label_atom_id
_struct_conn.ptnr1_label_comp_id
_struct_conn.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
_chem_comp.pdbx_synonyms
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
D
GLC
400
n
B
GLC
1
D
MAN
410
n
B
MAN
2
D
GAL
420
n
B
GAL
3
DGalpb
b-D-galactopyranose
b-D-Galp
Gal
DGlcpa
a-D-glucopyranose
a-D-Glcp
Glc
DManpa
a-D-mannopyranose
a-D-Manp
Man
1qm8 is the ground-state structure of bacteriorhodopsin determined at 2.5 angstrom.
Y
PDBJ
Y
PDBJ
2002-04-22
REL
oligosaccharide
DGalpb1-6DManpa1-2DGlcpa1-ROH
2
GMML
1.0
Glycam Condensed Sequence
WURCS=2.0/3,3,2/[a2122h-1a_1-5][a1122h-1a_1-5][a2112h-1b_1-5]/1-2-3/a2-b1_b6-c1
2
PDB2Glycan
1.1.0
WURCS
[][D-1-deoxy-Glcp]{[(2+1)][a-D-Manp]{[(6+1)][b-D-Galp]{}}}
2
PDB-CARE
LINUCS
C1
O2
MAN
GLC
2
1
2
O1
HO2
sing
C1
O6
GAL
MAN
3
2
2
O1
HO6
sing
n
n
n
RET
RETINAL
L3P
2,3-DI-O-PHYTANLY-3-SN-GLYCERO-1-PHOSPHORYL-3'-SN-GLYCEROL-1'-PHOSPHATE
L2P
2,3-DI-PHYTANYL-GLYCEROL
HOH
water
1QM8
PDB
experimental model
RET
250
3
RET
RET
250
A
L3P
260
4
L3P
L3P
260
A
L2P
270
5
L2P
L2P
270
A
L3P
280
4
L3P
L3P
280
A
L3P
290
4
L3P
L3P
290
A
L3P
300
4
L3P
L3P
300
A
HOH
600
6
HOH
HOH
600
A
HOH
601
6
HOH
HOH
601
A
HOH
602
6
HOH
HOH
602
A
HOH
603
6
HOH
HOH
603
A
HOH
604
6
HOH
HOH
604
A
HOH
605
6
HOH
HOH
605
A
HOH
606
6
HOH
HOH
606
A
HOH
607
6
HOH
HOH
607
A
HOH
608
6
HOH
HOH
608
A
HOH
609
6
HOH
HOH
609
A
HOH
610
6
HOH
HOH
610
A
HOH
611
6
HOH
HOH
611
A
HOH
612
6
HOH
HOH
612
A
HOH
613
6
HOH
HOH
613
A
HOH
614
6
HOH
HOH
614
A
HOH
615
6
HOH
HOH
615
A
HOH
616
6
HOH
HOH
616
A
HOH
617
6
HOH
HOH
617
A
HOH
618
6
HOH
HOH
618
A
HOH
619
6
HOH
HOH
619
A
HOH
620
6
HOH
HOH
620
A
HOH
621
6
HOH
HOH
621
A
HOH
622
6
HOH
HOH
622
A
HOH
623
6
HOH
HOH
623
A
HOH
624
6
HOH
HOH
624
A
HOH
625
6
HOH
HOH
625
A
HOH
626
6
HOH
HOH
626
A
HOH
627
6
HOH
HOH
627
A
HOH
628
6
HOH
HOH
628
A
HOH
629
6
HOH
HOH
629
A
HOH
630
6
HOH
HOH
630
A
HOH
631
6
HOH
HOH
631
A
HOH
632
6
HOH
HOH
632
A
HOH
633
6
HOH
HOH
633
A
HOH
634
6
HOH
HOH
634
A
HOH
635
6
HOH
HOH
635
A
HOH
636
6
HOH
HOH
636
A
HOH
637
6
HOH
HOH
637
A
HOH
638
6
HOH
HOH
638
A
HOH
639
6
HOH
HOH
639
A
HOH
640
6
HOH
HOH
640
A
n
1
1
A
n
2
2
A
n
3
3
A
n
4
4
A
THR
5
n
5
THR
5
A
GLY
6
n
6
GLY
6
A
ARG
7
n
7
ARG
7
A
PRO
8
n
8
PRO
8
A
GLU
9
n
9
GLU
9
A
TRP
10
n
10
TRP
10
A
ILE
11
n
11
ILE
11
A
TRP
12
n
12
TRP
12
A
LEU
13
n
13
LEU
13
A
ALA
14
n
14
ALA
14
A
LEU
15
n
15
LEU
15
A
GLY
16
n
16
GLY
16
A
THR
17
n
17
THR
17
A
ALA
18
n
18
ALA
18
A
LEU
19
n
19
LEU
19
A
MET
20
n
20
MET
20
A
GLY
21
n
21
GLY
21
A
LEU
22
n
22
LEU
22
A
GLY
23
n
23
GLY
23
A
THR
24
n
24
THR
24
A
LEU
25
n
25
LEU
25
A
TYR
26
n
26
TYR
26
A
PHE
27
n
27
PHE
27
A
LEU
28
n
28
LEU
28
A
VAL
29
n
29
VAL
29
A
LYS
30
n
30
LYS
30
A
GLY
31
n
31
GLY
31
A
MET
32
n
32
MET
32
A
GLY
33
n
33
GLY
33
A
VAL
34
n
34
VAL
34
A
SER
35
n
35
SER
35
A
ASP
36
n
36
ASP
36
A
PRO
37
n
37
PRO
37
A
ASP
38
n
38
ASP
38
A
ALA
39
n
39
ALA
39
A
LYS
40
n
40
LYS
40
A
LYS
41
n
41
LYS
41
A
PHE
42
n
42
PHE
42
A
TYR
43
n
43
TYR
43
A
ALA
44
n
44
ALA
44
A
ILE
45
n
45
ILE
45
A
THR
46
n
46
THR
46
A
THR
47
n
47
THR
47
A
LEU
48
n
48
LEU
48
A
VAL
49
n
49
VAL
49
A
PRO
50
n
50
PRO
50
A
ALA
51
n
51
ALA
51
A
ILE
52
n
52
ILE
52
A
ALA
53
n
53
ALA
53
A
PHE
54
n
54
PHE
54
A
THR
55
n
55
THR
55
A
MET
56
n
56
MET
56
A
TYR
57
n
57
TYR
57
A
LEU
58
n
58
LEU
58
A
SER
59
n
59
SER
59
A
MET
60
n
60
MET
60
A
LEU
61
n
61
LEU
61
A
LEU
62
n
62
LEU
62
A
GLY
63
n
63
GLY
63
A
TYR
64
n
64
TYR
64
A
GLY
65
n
65
GLY
65
A
LEU
66
n
66
LEU
66
A
THR
67
n
67
THR
67
A
MET
68
n
68
MET
68
A
VAL
69
n
69
VAL
69
A
PRO
70
n
70
PRO
70
A
PHE
71
n
71
PHE
71
A
GLY
72
n
72
GLY
72
A
GLY
73
n
73
GLY
73
A
GLU
74
n
74
GLU
74
A
GLN
75
n
75
GLN
75
A
ASN
76
n
76
ASN
76
A
PRO
77
n
77
PRO
77
A
ILE
78
n
78
ILE
78
A
TYR
79
n
79
TYR
79
A
TRP
80
n
80
TRP
80
A
ALA
81
n
81
ALA
81
A
ARG
82
n
82
ARG
82
A
TYR
83
n
83
TYR
83
A
ALA
84
n
84
ALA
84
A
ASP
85
n
85
ASP
85
A
TRP
86
n
86
TRP
86
A
LEU
87
n
87
LEU
87
A
PHE
88
n
88
PHE
88
A
THR
89
n
89
THR
89
A
THR
90
n
90
THR
90
A
PRO
91
n
91
PRO
91
A
LEU
92
n
92
LEU
92
A
LEU
93
n
93
LEU
93
A
LEU
94
n
94
LEU
94
A
LEU
95
n
95
LEU
95
A
ASP
96
n
96
ASP
96
A
LEU
97
n
97
LEU
97
A
ALA
98
n
98
ALA
98
A
LEU
99
n
99
LEU
99
A
LEU
100
n
100
LEU
100
A
VAL
101
n
101
VAL
101
A
ASP
102
n
102
ASP
102
A
ALA
103
n
103
ALA
103
A
ASP
104
n
104
ASP
104
A
GLN
105
n
105
GLN
105
A
GLY
106
n
106
GLY
106
A
THR
107
n
107
THR
107
A
ILE
108
n
108
ILE
108
A
LEU
109
n
109
LEU
109
A
ALA
110
n
110
ALA
110
A
LEU
111
n
111
LEU
111
A
VAL
112
n
112
VAL
112
A
GLY
113
n
113
GLY
113
A
ALA
114
n
114
ALA
114
A
ASP
115
n
115
ASP
115
A
GLY
116
n
116
GLY
116
A
ILE
117
n
117
ILE
117
A
MET
118
n
118
MET
118
A
ILE
119
n
119
ILE
119
A
GLY
120
n
120
GLY
120
A
THR
121
n
121
THR
121
A
GLY
122
n
122
GLY
122
A
LEU
123
n
123
LEU
123
A
VAL
124
n
124
VAL
124
A
GLY
125
n
125
GLY
125
A
ALA
126
n
126
ALA
126
A
LEU
127
n
127
LEU
127
A
THR
128
n
128
THR
128
A
LYS
129
n
129
LYS
129
A
VAL
130
n
130
VAL
130
A
TYR
131
n
131
TYR
131
A
SER
132
n
132
SER
132
A
TYR
133
n
133
TYR
133
A
ARG
134
n
134
ARG
134
A
PHE
135
n
135
PHE
135
A
VAL
136
n
136
VAL
136
A
TRP
137
n
137
TRP
137
A
TRP
138
n
138
TRP
138
A
ALA
139
n
139
ALA
139
A
ILE
140
n
140
ILE
140
A
SER
141
n
141
SER
141
A
THR
142
n
142
THR
142
A
ALA
143
n
143
ALA
143
A
ALA
144
n
144
ALA
144
A
MET
145
n
145
MET
145
A
LEU
146
n
146
LEU
146
A
TYR
147
n
147
TYR
147
A
ILE
148
n
148
ILE
148
A
LEU
149
n
149
LEU
149
A
TYR
150
n
150
TYR
150
A
VAL
151
n
151
VAL
151
A
LEU
152
n
152
LEU
152
A
PHE
153
n
153
PHE
153
A
PHE
154
n
154
PHE
154
A
GLY
155
n
155
GLY
155
A
PHE
156
n
156
PHE
156
A
THR
157
n
157
THR
157
A
SER
158
n
158
SER
158
A
LYS
159
n
159
LYS
159
A
ALA
160
n
160
ALA
160
A
GLU
161
n
161
GLU
161
A
SER
162
n
162
SER
162
A
MET
163
n
163
MET
163
A
ARG
164
n
164
ARG
164
A
PRO
165
n
165
PRO
165
A
GLU
166
n
166
GLU
166
A
VAL
167
n
167
VAL
167
A
ALA
168
n
168
ALA
168
A
SER
169
n
169
SER
169
A
THR
170
n
170
THR
170
A
PHE
171
n
171
PHE
171
A
LYS
172
n
172
LYS
172
A
VAL
173
n
173
VAL
173
A
LEU
174
n
174
LEU
174
A
ARG
175
n
175
ARG
175
A
ASN
176
n
176
ASN
176
A
VAL
177
n
177
VAL
177
A
THR
178
n
178
THR
178
A
VAL
179
n
179
VAL
179
A
VAL
180
n
180
VAL
180
A
LEU
181
n
181
LEU
181
A
TRP
182
n
182
TRP
182
A
SER
183
n
183
SER
183
A
ALA
184
n
184
ALA
184
A
TYR
185
n
185
TYR
185
A
PRO
186
n
186
PRO
186
A
VAL
187
n
187
VAL
187
A
VAL
188
n
188
VAL
188
A
TRP
189
n
189
TRP
189
A
LEU
190
n
190
LEU
190
A
ILE
191
n
191
ILE
191
A
GLY
192
n
192
GLY
192
A
SER
193
n
193
SER
193
A
GLU
194
n
194
GLU
194
A
GLY
195
n
195
GLY
195
A
ALA
196
n
196
ALA
196
A
GLY
197
n
197
GLY
197
A
ILE
198
n
198
ILE
198
A
VAL
199
n
199
VAL
199
A
PRO
200
n
200
PRO
200
A
LEU
201
n
201
LEU
201
A
ASN
202
n
202
ASN
202
A
ILE
203
n
203
ILE
203
A
GLU
204
n
204
GLU
204
A
THR
205
n
205
THR
205
A
LEU
206
n
206
LEU
206
A
LEU
207
n
207
LEU
207
A
PHE
208
n
208
PHE
208
A
MET
209
n
209
MET
209
A
VAL
210
n
210
VAL
210
A
LEU
211
n
211
LEU
211
A
ASP
212
n
212
ASP
212
A
VAL
213
n
213
VAL
213
A
SER
214
n
214
SER
214
A
ALA
215
n
215
ALA
215
A
LYS
216
n
216
LYS
216
A
VAL
217
n
217
VAL
217
A
GLY
218
n
218
GLY
218
A
PHE
219
n
219
PHE
219
A
GLY
220
n
220
GLY
220
A
LEU
221
n
221
LEU
221
A
ILE
222
n
222
ILE
222
A
LEU
223
n
223
LEU
223
A
LEU
224
n
224
LEU
224
A
ARG
225
n
225
ARG
225
A
SER
226
n
226
SER
226
A
ARG
227
n
227
ARG
227
A
ALA
228
n
228
ALA
228
A
ILE
229
n
229
ILE
229
A
PHE
230
n
230
PHE
230
A
GLY
231
n
231
GLY
231
A
n
232
232
A
n
233
233
A
n
234
234
A
n
235
235
A
n
236
236
A
n
237
237
A
n
238
238
A
n
239
239
A
n
240
240
A
n
241
241
A
n
242
242
A
n
243
243
A
n
244
244
A
n
245
245
A
n
246
246
A
n
247
247
A
n
248
248
A
author_defined_assembly
3
trimeric
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
-0.5000000000
-0.8660254038
0.0000000000
0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
2_655
-y+1,x-y,z
crystal symmetry operation
102.4000000000
0.0000000000
0.0000000000
-0.5000000000
0.8660254038
0.0000000000
-0.8660254038
-0.5000000000
0.0000000000
0.0000000000
0.0000000000
1.0000000000
3_665
-x+y+1,-x+1,z
crystal symmetry operation
51.2000000000
88.6810013475
0.0000000000
A
N
VAL
69
A
N
VAL
69
A
O
ASN
76
A
O
ASN
76
1
A
C4
L3P
280
F
C4
L3P
1
1
N
1
A
C5
L3P
280
F
C5
L3P
1
1
N
1
A
C6
L3P
280
F
C6
L3P
1
1
N
1
A
O5
L3P
280
F
O5
L3P
1
1
N
1
A
O6
L3P
280
F
O6
L3P
1
1
N
1
A
O4P
L3P
280
F
O4P
L3P
1
1
N
1
A
O5P
L3P
280
F
O5P
L3P
1
1
N
1
A
O6P
L3P
280
F
O6P
L3P
1
1
N
1
A
P2
L3P
280
F
P2
L3P
1
1
N
1
A
C21
L3P
280
F
C21
L3P
1
1
N
1
A
C22
L3P
280
F
C22
L3P
1
1
N
1
A
C23
L3P
280
F
C23
L3P
1
1
N
1
A
C24
L3P
280
F
C24
L3P
1
1
N
1
A
C25
L3P
280
F
C25
L3P
1
1
N
1
A
C26
L3P
280
F
C26
L3P
1
1
N
1
A
C27
L3P
280
F
C27
L3P
1
1
N
1
A
C28
L3P
280
F
C28
L3P
1
1
N
1
A
C29
L3P
280
F
C29
L3P
1
1
N
1
A
C30
L3P
280
F
C30
L3P
1
1
N
1
A
C4
L3P
290
G
C4
L3P
1
1
N
1
A
C5
L3P
290
G
C5
L3P
1
1
N
1
A
C6
L3P
290
G
C6
L3P
1
1
N
1
A
O5
L3P
290
G
O5
L3P
1
1
N
1
A
O6
L3P
290
G
O6
L3P
1
1
N
1
A
O4P
L3P
290
G
O4P
L3P
1
1
N
1
A
O5P
L3P
290
G
O5P
L3P
1
1
N
1
A
O6P
L3P
290
G
O6P
L3P
1
1
N
1
A
P2
L3P
290
G
P2
L3P
1
1
N
1
A
C4
L3P
300
H
C4
L3P
1
1
N
1
A
C5
L3P
300
H
C5
L3P
1
1
N
1
A
C6
L3P
300
H
C6
L3P
1
1
N
1
A
O5
L3P
300
H
O5
L3P
1
1
N
1
A
O6
L3P
300
H
O6
L3P
1
1
N
1
A
O4P
L3P
300
H
O4P
L3P
1
1
N
1
A
O5P
L3P
300
H
O5P
L3P
1
1
N
1
A
O6P
L3P
300
H
O6P
L3P
1
1
N
1
A
P2
L3P
300
H
P2
L3P
1
1
N
1
A
GLN
1
A
GLN
1
1
Y
1
A
ALA
2
A
ALA
2
1
Y
1
A
GLN
3
A
GLN
3
1
Y
1
A
ILE
4
A
ILE
4
1
Y
1
A
GLU
232
A
GLU
232
1
Y
1
A
ALA
233
A
ALA
233
1
Y
1
A
GLU
234
A
GLU
234
1
Y
1
A
ALA
235
A
ALA
235
1
Y
1
A
PRO
236
A
PRO
236
1
Y
1
A
GLU
237
A
GLU
237
1
Y
1
A
PRO
238
A
PRO
238
1
Y
1
A
SER
239
A
SER
239
1
Y
1
A
ALA
240
A
ALA
240
1
Y
1
A
GLY
241
A
GLY
241
1
Y
1
A
ASP
242
A
ASP
242
1
Y
1
A
GLY
243
A
GLY
243
1
Y
1
A
ALA
244
A
ALA
244
1
Y
1
A
ALA
245
A
ALA
245
1
Y
1
A
ALA
246
A
ALA
246
1
Y
1
A
THR
247
A
THR
247
1
Y
1
A
SER
248
A
SER
248
1
Y
1
B
C1
GLC
1
PLANAR
1
A
ARG
7
-165.90
-53.24
1
A
VAL
29
-83.71
46.81
1
A
LYS
30
-155.86
-26.94
1
A
LYS
216
-122.36
-67.84
56.4
-9.69
-5.55
-9.69
19.39
0.275
0.251
0.251
0.251
2.3
28.4
792
16024
15703
5
98
random
1
anisotropic
THROUGHOUT
0
MOLECULAR REPLACEMENT
1qm8
Engh & Huber
0.35
0.32
5
0.37
0.33
2.3
28.4
41
2095
298
0
1756
0.0076
1.16
17.7
0.83
0.3546
0.3155
2.38
63
1254
1624
10
4
83.9
0.333
0.295
2.59
86
1476
10
0.244
0.228
2.90
79
1493
10
0.253
0.223
3.43
96
1490
10
0.255
0.215
4.95
79
1563
10
50.7
2.30
28.4
1IW6
16008
15703
0.079
0.079
1
5.9
11.6
99.7
0.487
2.30
2.42
1.6
2258
0.487
11.8
99.7
data reduction
MOSFLM
data scaling
SCALA
refinement
CNS
data scaling
CCP4
(SCALA)
phasing
CNS
Crystal Structure of the Ground State of Bacteriorhodopsin
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
4
N
N
4
N
N
4
N
N
6
N
N
The biological assembly is a trimer generated from the monomer in the asymmetric unit by the operations: 1-y, x-y, z and 1-x+y, 1-x, z
A
GLU
9
A
GLU
9
HELX_P
A
VAL
29
A
VAL
29
1
1
21
A
ASP
36
A
ASP
36
HELX_P
A
LEU
62
A
LEU
62
1
2
27
A
TRP
80
A
TRP
80
HELX_P
A
ASP
102
A
ASP
102
1
3
23
A
ASP
104
A
ASP
104
HELX_P
A
THR
128
A
THR
128
1
4
25
A
VAL
130
A
VAL
130
HELX_P
A
PHE
154
A
PHE
154
1
5
25
A
PHE
154
A
PHE
154
HELX_P
A
GLU
161
A
GLU
161
1
6
8
A
ARG
164
A
ARG
164
HELX_P
A
SER
183
A
SER
183
1
7
20
A
SER
183
A
SER
183
HELX_P
A
GLY
192
A
GLY
192
1
8
10
A
PRO
200
A
PRO
200
HELX_P
A
ARG
225
A
ARG
225
1
9
26
covale
1.357
one
A
LYS
216
A
NZ
LYS
216
1_555
A
RET
250
C
C15
RET
1_555
covale
1.437
one
A
L2P
270
E
O3
L2P
1_555
B
GLC
1
B
C1
GLC
1_555
covale
1.435
both
B
GLC
1
B
O2
GLC
1_555
B
MAN
2
B
C1
MAN
1_555
covale
1.432
both
B
MAN
2
B
O6
MAN
1_555
B
GAL
3
B
C1
GAL
1_555
PROTON TRANSPORT
7 Helix, RIKEN Structural Genomics/Proteomics Initiative, RSGI, Structural Genomics, PROTON TRANSPORT
BACR_HALHA
UNP
1
1
P02945
QAQITGRPEWIWLALGTALMGLGTLYFLVKGMGVSDPDAKKFYAITTLVPAIAFTMYLSMLLGYGLTMVPFGGEQNPIYW
ARYADWLFTTPLLLLDLALLVDADQGTILALVGADGIMIGTGLVGALTKVYSYRFVWWAISTAAMLYILYVLFFGFTSKA
ESMRPEVASTFKVLRNVTVVLWSAYPVVWLIGSEGAGIVPLNIETLLFMVLDVSAKVGFGLILLRSRAIFGEAEAPEPSA
GDGAAATS
14
261
1IW6
1
248
P02945
A
1
1
248
2
anti-parallel
A
LEU
66
A
LEU
66
A
PRO
70
A
PRO
70
A
GLN
75
A
GLN
75
A
TYR
79
A
TYR
79
177
P 6 2 2