0.016956
0.009790
0.000000
0.000000
0.019579
0.000000
0.000000
0.000000
0.009956
0.00000
0.00000
0.00000
Nosrati, M.
Geiger, J.H.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
58.975
58.975
100.443
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
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
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
N
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
N
N
89
S
C
N
90
N
C
N
91
N
O
N
92
N
C
N
93
N
C
N
94
N
C
N
95
N
O
N
96
N
N
N
97
N
O
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
H
N
104
N
H
N
105
N
H
N
106
N
H
N
107
N
H
N
108
N
N
N
109
S
C
N
110
N
C
N
111
N
O
N
112
N
C
N
113
N
C
N
114
N
C
N
115
N
O
N
116
N
O
N
117
N
O
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
N
N
128
N
C
N
129
N
C
N
130
N
O
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
O
N
138
N
H
N
139
N
H
N
140
N
N
N
141
S
C
N
142
N
C
N
143
N
O
N
144
S
C
N
145
N
C
N
146
N
C
N
147
N
C
N
148
N
O
N
149
N
H
N
150
N
H
N
151
N
H
N
152
N
H
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
H
N
159
N
H
N
160
N
H
N
161
N
H
N
162
N
N
N
163
S
C
N
164
N
C
N
165
N
O
N
166
N
C
N
167
N
C
N
168
N
C
N
169
N
C
N
170
N
O
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
N
N
185
S
C
N
186
N
C
N
187
N
O
N
188
N
C
N
189
N
C
N
190
N
C
N
191
N
C
N
192
N
N
N
193
N
O
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
H
N
205
N
H
N
206
N
H
N
207
N
H
N
208
N
H
N
209
N
N
N
210
S
C
N
211
N
C
N
212
N
O
N
213
N
C
N
214
N
C
N
215
N
S
N
216
N
C
N
217
N
O
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
H
N
227
N
H
N
228
N
H
N
229
N
N
N
230
S
C
N
231
N
C
N
232
N
O
N
233
N
C
Y
234
N
C
Y
235
N
C
Y
236
N
C
Y
237
N
C
Y
238
N
C
Y
239
N
C
N
240
N
O
N
241
N
H
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
N
N
253
S
C
N
254
N
C
N
255
N
O
N
256
N
C
N
257
N
C
N
258
N
C
N
259
N
O
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
C
N
270
N
C
N
271
N
C
N
272
N
C
N
273
N
C
N
274
N
C
N
275
N
C
N
276
N
C
N
277
N
C
N
278
N
C
N
279
N
C
N
280
N
C
N
281
N
C
N
282
N
C
N
283
N
C
N
284
N
O
N
285
N
C
N
286
N
C
N
287
N
C
N
288
N
C
N
289
N
C
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
N
N
319
S
C
N
320
N
C
N
321
N
O
N
322
N
C
N
323
N
O
N
324
N
O
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
N
N
333
S
C
N
334
N
C
N
335
N
O
N
336
R
C
N
337
N
O
N
338
N
C
N
339
N
O
N
340
N
H
N
341
N
H
N
342
N
H
N
343
N
H
N
344
N
H
N
345
N
H
N
346
N
H
N
347
N
H
N
348
N
H
N
349
N
N
N
350
S
C
N
351
N
C
N
352
N
O
N
353
N
C
Y
354
N
C
Y
355
N
C
Y
356
N
C
Y
357
N
N
Y
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
Y
362
N
C
N
363
N
O
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
H
N
368
N
H
N
369
N
H
N
370
N
H
N
371
N
H
N
372
N
H
N
373
N
H
N
374
N
H
N
375
N
H
N
376
N
N
N
377
S
C
N
378
N
C
N
379
N
O
N
380
N
C
Y
381
N
C
Y
382
N
C
Y
383
N
C
Y
384
N
C
Y
385
N
C
Y
386
N
C
N
387
N
O
N
388
N
O
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
N
N
401
S
C
N
402
N
C
N
403
N
O
N
404
N
C
N
405
N
C
N
406
N
C
N
407
N
O
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
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
doub
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
doub
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
doub
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
doub
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
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
doub
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
sing
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
N
153
N
sing
N
154
N
sing
N
155
N
sing
N
156
N
sing
N
157
N
sing
N
158
N
doub
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
sing
N
172
N
sing
N
173
N
sing
N
174
N
sing
N
175
N
sing
N
176
N
sing
N
177
N
sing
N
178
N
sing
N
179
N
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
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
doub
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
doub
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
Y
227
N
doub
Y
228
N
sing
Y
229
N
sing
N
230
N
sing
Y
231
N
doub
N
232
N
sing
Y
233
N
doub
N
234
N
sing
Y
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
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
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
doub
N
270
N
sing
N
271
N
sing
N
272
E
doub
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
E
doub
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
E
doub
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
E
doub
N
285
N
sing
N
286
N
sing
N
287
N
sing
N
288
N
doub
N
289
N
sing
N
290
N
sing
N
291
N
sing
N
292
N
sing
N
293
N
sing
N
294
N
sing
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
N
299
N
sing
N
300
N
sing
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
doub
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
doub
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
doub
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
Y
345
N
doub
Y
346
N
sing
Y
347
N
sing
N
348
N
sing
Y
349
N
doub
Y
350
N
sing
Y
351
N
sing
N
352
N
sing
Y
353
N
sing
Y
354
N
doub
N
355
N
sing
Y
356
N
doub
N
357
N
sing
Y
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
doub
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
Y
373
N
doub
Y
374
N
sing
Y
375
N
sing
N
376
N
sing
Y
377
N
doub
N
378
N
sing
Y
379
N
doub
N
380
N
sing
Y
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
doub
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
US
J.Am.Chem.Soc.
JACSAT
1520-5126
138
8802
8808
10.1021/jacs.6b03681
27310917
A Photoisomerizing Rhodopsin Mimic Observed at Atomic Resolution.
2016
10.2210/pdb4ygz/pdb
pdb_00004ygz
100
1
CCD
2014-07-13
MARMOSAIC 225 mm CCD
SINGLE WAVELENGTH
M
x-ray
1
0.97872
1.0
21-ID-F
APS
0.97872
SYNCHROTRON
APS BEAMLINE 21-ID-F
15578.792
Cellular retinoic acid-binding protein 2
R111K, Y134F, T54V, R132Q, P39Y, R59Y
1
man
polymer
284.436
RETINAL
1
syn
non-polymer
18.015
water
123
nat
water
Cellular retinoic acid-binding protein II,CRABP-II
no
no
PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKYAVEIKQEGDTFYIKVSTTVYTTEINFKVGEEFEEQTVDGRP
CKSLVKWESENKMVCEQKLLKGEGPKTSWTKELTNDGELILTMTADDVVCTQVFVRE
PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKYAVEIKQEGDTFYIKVSTTVYTTEINFKVGEEFEEQTVDGRP
CKSLVKWESENKMVCEQKLLKGEGPKTSWTKELTNDGELILTMTADDVVCTQVFVRE
A
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
Human
sample
1
137
CRABP2
9606
Homo sapiens
469008
Escherichia coli
BL21(DE3)
Plasmid
Biological sequence
pET17b
3.24
62.00
VAPOR DIFFUSION, HANGING DROP
12% PEG3350, 0.1M Malonate pH=6.0
277
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_oper_list
repository
Initial release
Structure summary
Database references
Database references
Data collection
Database references
Derived calculations
Refinement description
1
0
2016-03-02
1
1
2016-06-15
1
2
2016-06-29
1
3
2016-08-03
1
4
2023-09-27
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_struct_oper_list.symmetry_operation
N
RCSB
Y
RCSB
2015-02-26
REL
REL
RET
RETINAL
HOH
water
2G7B
PDB
experimental model
RET
1
2
RET
RET
201
A
HOH
44
3
HOH
HOH
301
A
HOH
26
3
HOH
HOH
302
A
HOH
85
3
HOH
HOH
303
A
HOH
112
3
HOH
HOH
304
A
HOH
21
3
HOH
HOH
305
A
HOH
104
3
HOH
HOH
306
A
HOH
36
3
HOH
HOH
307
A
HOH
31
3
HOH
HOH
308
A
HOH
46
3
HOH
HOH
309
A
HOH
114
3
HOH
HOH
310
A
HOH
45
3
HOH
HOH
311
A
HOH
86
3
HOH
HOH
312
A
HOH
11
3
HOH
HOH
313
A
HOH
17
3
HOH
HOH
314
A
HOH
51
3
HOH
HOH
315
A
HOH
119
3
HOH
HOH
316
A
HOH
9
3
HOH
HOH
317
A
HOH
113
3
HOH
HOH
318
A
HOH
83
3
HOH
HOH
319
A
HOH
3
3
HOH
HOH
320
A
HOH
108
3
HOH
HOH
321
A
HOH
41
3
HOH
HOH
322
A
HOH
24
3
HOH
HOH
323
A
HOH
95
3
HOH
HOH
324
A
HOH
2
3
HOH
HOH
325
A
HOH
59
3
HOH
HOH
326
A
HOH
82
3
HOH
HOH
327
A
HOH
62
3
HOH
HOH
328
A
HOH
38
3
HOH
HOH
329
A
HOH
18
3
HOH
HOH
330
A
HOH
67
3
HOH
HOH
331
A
HOH
68
3
HOH
HOH
332
A
HOH
123
3
HOH
HOH
333
A
HOH
22
3
HOH
HOH
334
A
HOH
43
3
HOH
HOH
335
A
HOH
63
3
HOH
HOH
336
A
HOH
1
3
HOH
HOH
337
A
HOH
4
3
HOH
HOH
338
A
HOH
5
3
HOH
HOH
339
A
HOH
6
3
HOH
HOH
340
A
HOH
7
3
HOH
HOH
341
A
HOH
8
3
HOH
HOH
342
A
HOH
10
3
HOH
HOH
343
A
HOH
12
3
HOH
HOH
344
A
HOH
13
3
HOH
HOH
345
A
HOH
14
3
HOH
HOH
346
A
HOH
15
3
HOH
HOH
347
A
HOH
16
3
HOH
HOH
348
A
HOH
19
3
HOH
HOH
349
A
HOH
20
3
HOH
HOH
350
A
HOH
23
3
HOH
HOH
351
A
HOH
25
3
HOH
HOH
352
A
HOH
27
3
HOH
HOH
353
A
HOH
28
3
HOH
HOH
354
A
HOH
29
3
HOH
HOH
355
A
HOH
30
3
HOH
HOH
356
A
HOH
32
3
HOH
HOH
357
A
HOH
33
3
HOH
HOH
358
A
HOH
34
3
HOH
HOH
359
A
HOH
35
3
HOH
HOH
360
A
HOH
37
3
HOH
HOH
361
A
HOH
39
3
HOH
HOH
362
A
HOH
40
3
HOH
HOH
363
A
HOH
42
3
HOH
HOH
364
A
HOH
47
3
HOH
HOH
365
A
HOH
48
3
HOH
HOH
366
A
HOH
49
3
HOH
HOH
367
A
HOH
50
3
HOH
HOH
368
A
HOH
52
3
HOH
HOH
369
A
HOH
53
3
HOH
HOH
370
A
HOH
54
3
HOH
HOH
371
A
HOH
55
3
HOH
HOH
372
A
HOH
56
3
HOH
HOH
373
A
HOH
57
3
HOH
HOH
374
A
HOH
58
3
HOH
HOH
375
A
HOH
60
3
HOH
HOH
376
A
HOH
61
3
HOH
HOH
377
A
HOH
64
3
HOH
HOH
378
A
HOH
65
3
HOH
HOH
379
A
HOH
66
3
HOH
HOH
380
A
HOH
69
3
HOH
HOH
381
A
HOH
70
3
HOH
HOH
382
A
HOH
71
3
HOH
HOH
383
A
HOH
72
3
HOH
HOH
384
A
HOH
73
3
HOH
HOH
385
A
HOH
74
3
HOH
HOH
386
A
HOH
75
3
HOH
HOH
387
A
HOH
76
3
HOH
HOH
388
A
HOH
77
3
HOH
HOH
389
A
HOH
78
3
HOH
HOH
390
A
HOH
79
3
HOH
HOH
391
A
HOH
80
3
HOH
HOH
392
A
HOH
81
3
HOH
HOH
393
A
HOH
84
3
HOH
HOH
394
A
HOH
87
3
HOH
HOH
395
A
HOH
88
3
HOH
HOH
396
A
HOH
89
3
HOH
HOH
397
A
HOH
90
3
HOH
HOH
398
A
HOH
91
3
HOH
HOH
399
A
HOH
92
3
HOH
HOH
400
A
HOH
93
3
HOH
HOH
401
A
HOH
94
3
HOH
HOH
402
A
HOH
96
3
HOH
HOH
403
A
HOH
97
3
HOH
HOH
404
A
HOH
98
3
HOH
HOH
405
A
HOH
99
3
HOH
HOH
406
A
HOH
100
3
HOH
HOH
407
A
HOH
101
3
HOH
HOH
408
A
HOH
102
3
HOH
HOH
409
A
HOH
103
3
HOH
HOH
410
A
HOH
105
3
HOH
HOH
411
A
HOH
106
3
HOH
HOH
412
A
HOH
107
3
HOH
HOH
413
A
HOH
109
3
HOH
HOH
414
A
HOH
110
3
HOH
HOH
415
A
HOH
111
3
HOH
HOH
416
A
HOH
115
3
HOH
HOH
417
A
HOH
116
3
HOH
HOH
418
A
HOH
117
3
HOH
HOH
419
A
HOH
118
3
HOH
HOH
420
A
HOH
120
3
HOH
HOH
421
A
HOH
121
3
HOH
HOH
422
A
HOH
122
3
HOH
HOH
423
A
PRO
1
n
1
PRO
1
A
ASN
2
n
2
ASN
2
A
PHE
3
n
3
PHE
3
A
SER
4
n
4
SER
4
A
GLY
5
n
5
GLY
5
A
ASN
6
n
6
ASN
6
A
TRP
7
n
7
TRP
7
A
LYS
8
n
8
LYS
8
A
ILE
9
n
9
ILE
9
A
ILE
10
n
10
ILE
10
A
ARG
11
n
11
ARG
11
A
SER
12
n
12
SER
12
A
GLU
13
n
13
GLU
13
A
ASN
14
n
14
ASN
14
A
PHE
15
n
15
PHE
15
A
GLU
16
n
16
GLU
16
A
GLU
17
n
17
GLU
17
A
LEU
18
n
18
LEU
18
A
LEU
19
n
19
LEU
19
A
LYS
20
n
20
LYS
20
A
VAL
21
n
21
VAL
21
A
LEU
22
n
22
LEU
22
A
GLY
23
n
23
GLY
23
A
VAL
24
n
24
VAL
24
A
ASN
25
n
25
ASN
25
A
VAL
26
n
26
VAL
26
A
MET
27
n
27
MET
27
A
LEU
28
n
28
LEU
28
A
ARG
29
n
29
ARG
29
A
LYS
30
n
30
LYS
30
A
ILE
31
n
31
ILE
31
A
ALA
32
n
32
ALA
32
A
VAL
33
n
33
VAL
33
A
ALA
34
n
34
ALA
34
A
ALA
35
n
35
ALA
35
A
ALA
36
n
36
ALA
36
A
SER
37
n
37
SER
37
A
LYS
38
n
38
LYS
38
A
TYR
39
n
39
TYR
39
A
ALA
40
n
40
ALA
40
A
VAL
41
n
41
VAL
41
A
GLU
42
n
42
GLU
42
A
ILE
43
n
43
ILE
43
A
LYS
44
n
44
LYS
44
A
GLN
45
n
45
GLN
45
A
GLU
46
n
46
GLU
46
A
GLY
47
n
47
GLY
47
A
ASP
48
n
48
ASP
48
A
THR
49
n
49
THR
49
A
PHE
50
n
50
PHE
50
A
TYR
51
n
51
TYR
51
A
ILE
52
n
52
ILE
52
A
LYS
53
n
53
LYS
53
A
VAL
54
n
54
VAL
54
A
SER
55
n
55
SER
55
A
THR
56
n
56
THR
56
A
THR
57
n
57
THR
57
A
VAL
58
n
58
VAL
58
A
TYR
59
n
59
TYR
59
A
THR
60
n
60
THR
60
A
THR
61
n
61
THR
61
A
GLU
62
n
62
GLU
62
A
ILE
63
n
63
ILE
63
A
ASN
64
n
64
ASN
64
A
PHE
65
n
65
PHE
65
A
LYS
66
n
66
LYS
66
A
VAL
67
n
67
VAL
67
A
GLY
68
n
68
GLY
68
A
GLU
69
n
69
GLU
69
A
GLU
70
n
70
GLU
70
A
PHE
71
n
71
PHE
71
A
GLU
72
n
72
GLU
72
A
GLU
73
n
73
GLU
73
A
GLN
74
n
74
GLN
74
A
THR
75
n
75
THR
75
A
VAL
76
n
76
VAL
76
A
ASP
77
n
77
ASP
77
A
GLY
78
n
78
GLY
78
A
ARG
79
n
79
ARG
79
A
PRO
80
n
80
PRO
80
A
CYS
81
n
81
CYS
81
A
LYS
82
n
82
LYS
82
A
SER
83
n
83
SER
83
A
LEU
84
n
84
LEU
84
A
VAL
85
n
85
VAL
85
A
LYS
86
n
86
LYS
86
A
TRP
87
n
87
TRP
87
A
GLU
88
n
88
GLU
88
A
SER
89
n
89
SER
89
A
GLU
90
n
90
GLU
90
A
ASN
91
n
91
ASN
91
A
LYS
92
n
92
LYS
92
A
MET
93
n
93
MET
93
A
VAL
94
n
94
VAL
94
A
CYS
95
n
95
CYS
95
A
GLU
96
n
96
GLU
96
A
GLN
97
n
97
GLN
97
A
LYS
98
n
98
LYS
98
A
LEU
99
n
99
LEU
99
A
LEU
100
n
100
LEU
100
A
LYS
101
n
101
LYS
101
A
GLY
102
n
102
GLY
102
A
GLU
103
n
103
GLU
103
A
GLY
104
n
104
GLY
104
A
PRO
105
n
105
PRO
105
A
LYS
106
n
106
LYS
106
A
THR
107
n
107
THR
107
A
SER
108
n
108
SER
108
A
TRP
109
n
109
TRP
109
A
THR
110
n
110
THR
110
A
LYS
111
n
111
LYS
111
A
GLU
112
n
112
GLU
112
A
LEU
113
n
113
LEU
113
A
THR
114
n
114
THR
114
A
ASN
115
n
115
ASN
115
A
ASP
116
n
116
ASP
116
A
GLY
117
n
117
GLY
117
A
GLU
118
n
118
GLU
118
A
LEU
119
n
119
LEU
119
A
ILE
120
n
120
ILE
120
A
LEU
121
n
121
LEU
121
A
THR
122
n
122
THR
122
A
MET
123
n
123
MET
123
A
THR
124
n
124
THR
124
A
ALA
125
n
125
ALA
125
A
ASP
126
n
126
ASP
126
A
ASP
127
n
127
ASP
127
A
VAL
128
n
128
VAL
128
A
VAL
129
n
129
VAL
129
A
CYS
130
n
130
CYS
130
A
THR
131
n
131
THR
131
A
GLN
132
n
132
GLN
132
A
VAL
133
n
133
VAL
133
A
PHE
134
n
134
PHE
134
A
VAL
135
n
135
VAL
135
A
ARG
136
n
136
ARG
136
A
GLU
137
n
137
GLU
137
A
author_defined_assembly
1
monomeric
software_defined_assembly
PISA
2
dimeric
3260
-24
13760
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
4_645
y+1,x-1,-z
crystal symmetry operation
88.4625000000
-51.0738481882
0.0000000000
A
O
ILE
63
A
O
ILE
63
A
N
ILE
52
A
N
ILE
52
A
O
TYR
51
A
O
TYR
51
A
N
LYS
44
A
N
LYS
44
A
O
VAL
41
A
O
VAL
41
A
N
TRP
7
A
N
TRP
7
A
N
LYS
8
A
N
LYS
8
A
O
VAL
135
A
O
VAL
135
A
O
CYS
130
A
O
CYS
130
A
N
MET
123
A
N
MET
123
A
O
ILE
120
A
O
ILE
120
A
N
GLU
112
A
N
GLU
112
A
O
TRP
109
A
O
TRP
109
A
N
CYS
95
A
N
CYS
95
A
O
LYS
92
A
O
LYS
92
A
N
GLU
88
A
N
GLU
88
A
O
SER
83
A
O
SER
83
A
N
PHE
71
A
N
PHE
71
1
A
A
OE1
O
GLU
HOH
137
389
2.13
1
A
ASN
2
-97.81
51.50
1
A
THR
56
-119.50
-167.24
1
A
GLU
73
-145.90
-153.26
1
A
SER
89
-171.28
-170.32
1
A
ASP
126
54.82
-112.41
-0.2565
0.0000
-0.0000
-0.2565
0.0000
0.5131
0.2545
0.2016
0.2042
2.060
45.526
633
13010
4.87
99.92
0.37
1
FREE R-VALUE
1.39
MOLECULAR REPLACEMENT
24.55
0.73
1.00
2G7B
ML
FLAT BULK SOLVENT MODEL
36.115
0.328
2.060
45.526
123
1235
20
0
1092
0.009
1147
1.228
1552
15.737
437
0.091
177
0.004
199
0.2569
0.2240
2.2195
117
2417
100.00
0.2587
0.2298
2.4429
123
2459
100.00
0.3156
0.2278
2.7963
121
2437
100.00
0.2284
0.2061
3.5229
134
2476
100.00
0.2502
0.1811
45.5374
138
2588
100.00
2.06
50
4YGZ
13048
0.068
0.053
1
40.72
10.8
99.9
0.533
2.06
2.1
5.12
1
10.9
99.8
refinement
PHENIX
(phenix.refine: 1.7.2_869)
data reduction
HKL-2000
data scaling
HKL-2000
phasing
MOLREP
CRYSTAL STRUCTURE OF THE R111K:Y134F:T54V:R132Q:P39Y:R59Y MUTANT OF HUMAN CELLULAR RETINOIC ACID BINDING PROTEIN II WITH RETINAL AT 2.06 ANGSTROM RESOLUTION - VISIBLE LIGHT IRRADIATED CRYSTAL -3RD CYCLE
1
N
N
2
N
N
3
N
N
A
ASN
14
A
ASN
14
HELX_P
A
LEU
22
A
LEU
22
1
AA1
9
A
ASN
25
A
ASN
25
HELX_P
A
ALA
36
A
ALA
36
1
AA2
12
covale
1.267
one
A
LYS
111
A
NZ
LYS
111
1_555
A
RET
201
B
C15
RET
1_555
TRANSPORT PROTEIN
Photo swithcable protein, Retinal isomerization, Retinal iminium protonated Schiff base pKa change, protein engineering, TRANSPORT PROTEIN
RABP2_HUMAN
UNP
1
2
P29373
PNFSGNWKIIRSENFEELLKVLGVNVMLRKIAVAAASKPAVEIKQEGDTFYIKTSTTVRTTEINFKVGEEFEEQTVDGRP
CKSLVKWESENKMVCEQKLLKGEGPKTSWTRELTNDGELILTMTADDVVCTRVYVRE
2
138
4YGZ
1
137
P29373
A
1
1
137
1
PRO
engineered mutation
TYR
39
4YGZ
A
P29373
UNP
40
39
1
THR
engineered mutation
VAL
54
4YGZ
A
P29373
UNP
55
54
1
ARG
engineered mutation
TYR
59
4YGZ
A
P29373
UNP
60
59
1
ARG
engineered mutation
LYS
111
4YGZ
A
P29373
UNP
112
111
1
ARG
engineered mutation
GLN
132
4YGZ
A
P29373
UNP
133
132
1
TYR
engineered mutation
PHE
134
4YGZ
A
P29373
UNP
135
134
10
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
THR
60
A
THR
60
A
LYS
66
A
LYS
66
A
THR
49
A
THR
49
A
SER
55
A
SER
55
A
ALA
40
A
ALA
40
A
GLU
46
A
GLU
46
A
GLY
5
A
GLY
5
A
GLU
13
A
GLU
13
A
VAL
128
A
VAL
128
A
ARG
136
A
ARG
136
A
LEU
119
A
LEU
119
A
ALA
125
A
ALA
125
A
THR
107
A
THR
107
A
LEU
113
A
LEU
113
A
LYS
92
A
LYS
92
A
LEU
99
A
LEU
99
A
PRO
80
A
PRO
80
A
SER
89
A
SER
89
A
PHE
71
A
PHE
71
A
GLN
74
A
GLN
74
binding site for residue RET A 201
A
RET
201
Software
8
A
PHE
15
A
PHE
15
8
1_555
A
MET
27
A
MET
27
8
4_645
A
ILE
31
A
ILE
31
8
4_645
A
TYR
39
A
TYR
39
8
1_555
A
THR
56
A
THR
56
8
1_555
A
VAL
76
A
VAL
76
8
1_555
A
LYS
111
A
LYS
111
8
1_555
A
MET
123
A
MET
123
8
1_555
152
P 31 2 1