0.024641
0.014227
0.000000
0.000000
0.028454
0.000000
0.000000
0.000000
0.008489
0.000000
0.000000
0.000000
van Aalten, D.M.F.
Crielaard, W.
Hellingwerf, K.J.
Joshua-Tor, L.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
40.582
40.582
117.801
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
C9 H8 O4
180.157
CAFFEIC ACID
3,4-DIHYDROXYCINNAMIC ACID
non-polymer
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
C4 H10
58.122
N-BUTANE
non-polymer
C9 H11 N O2
165.189
y
PHENYLALANINE
L-peptide linking
C5 H9 N O2
115.130
y
PROLINE
L-peptide linking
C3 H7 N O3
105.093
y
SERINE
L-peptide linking
C4 H9 N O3
119.119
y
THREONINE
L-peptide linking
C11 H12 N2 O2
204.225
y
TRYPTOPHAN
L-peptide linking
C9 H11 N O3
181.189
y
TYROSINE
L-peptide linking
C5 H11 N O2
117.146
y
VALINE
L-peptide linking
N
1
N
N
N
2
S
C
N
3
N
C
N
4
N
O
N
5
N
C
N
6
N
O
N
7
N
H
N
8
N
H
N
9
N
H
N
10
N
H
N
11
N
H
N
12
N
H
N
13
N
H
N
14
N
N
N
15
S
C
N
16
N
C
N
17
N
O
N
18
N
C
N
19
N
C
N
20
N
C
N
21
N
N
N
22
N
C
N
23
N
N
N
24
N
N
N
25
N
O
N
26
N
H
N
27
N
H
N
28
N
H
N
29
N
H
N
30
N
H
N
31
N
H
N
32
N
H
N
33
N
H
N
34
N
H
N
35
N
H
N
36
N
H
N
37
N
H
N
38
N
H
N
39
N
H
N
40
N
H
N
41
N
N
N
42
S
C
N
43
N
C
N
44
N
O
N
45
N
C
N
46
N
C
N
47
N
O
N
48
N
N
N
49
N
O
N
50
N
H
N
51
N
H
N
52
N
H
N
53
N
H
N
54
N
H
N
55
N
H
N
56
N
H
N
57
N
H
N
58
N
N
N
59
S
C
N
60
N
C
N
61
N
O
N
62
N
C
N
63
N
C
N
64
N
O
N
65
N
O
N
66
N
O
N
67
N
H
N
68
N
H
N
69
N
H
N
70
N
H
N
71
N
H
N
72
N
H
N
73
N
H
N
74
N
N
N
75
R
C
N
76
N
C
N
77
N
O
N
78
N
C
N
79
N
S
N
80
N
O
N
81
N
H
N
82
N
H
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
C
N
89
N
O
N
90
N
C
N
91
N
C
Y
92
N
C
Y
93
N
C
Y
94
N
C
Y
95
N
C
Y
96
N
C
Y
97
N
C
N
98
N
O
N
99
N
O
N
100
N
O
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
N
N
110
S
C
N
111
N
C
N
112
N
O
N
113
N
C
N
114
N
C
N
115
N
C
N
116
N
O
N
117
N
N
N
118
N
O
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
N
N
130
S
C
N
131
N
C
N
132
N
O
N
133
N
C
N
134
N
C
N
135
N
C
N
136
N
O
N
137
N
O
N
138
N
O
N
139
N
H
N
140
N
H
N
141
N
H
N
142
N
H
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
N
N
149
N
C
N
150
N
C
N
151
N
O
N
152
N
O
N
153
N
H
N
154
N
H
N
155
N
H
N
156
N
H
N
157
N
H
N
158
N
N
N
159
S
C
N
160
N
C
N
161
N
O
N
162
N
C
Y
163
N
C
Y
164
N
N
Y
165
N
C
Y
166
N
C
Y
167
N
N
N
168
N
O
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
H
N
173
N
H
N
174
N
H
N
175
N
H
N
176
N
H
N
177
N
H
N
178
N
H
N
179
N
O
N
180
N
H
N
181
N
H
N
182
N
N
N
183
S
C
N
184
N
C
N
185
N
O
N
186
S
C
N
187
N
C
N
188
N
C
N
189
N
C
N
190
N
O
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
H
N
196
N
H
N
197
N
H
N
198
N
H
N
199
N
H
N
200
N
H
N
201
N
H
N
202
N
H
N
203
N
H
N
204
N
N
N
205
S
C
N
206
N
C
N
207
N
O
N
208
N
C
N
209
N
C
N
210
N
C
N
211
N
C
N
212
N
O
N
213
N
H
N
214
N
H
N
215
N
H
N
216
N
H
N
217
N
H
N
218
N
H
N
219
N
H
N
220
N
H
N
221
N
H
N
222
N
H
N
223
N
H
N
224
N
H
N
225
N
H
N
226
N
N
N
227
S
C
N
228
N
C
N
229
N
O
N
230
N
C
N
231
N
C
N
232
N
C
N
233
N
C
N
234
N
N
N
235
N
O
N
236
N
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
H
N
242
N
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
N
N
252
S
C
N
253
N
C
N
254
N
O
N
255
N
C
N
256
N
C
N
257
N
S
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
H
N
270
N
H
N
271
N
C
N
272
N
C
N
273
N
C
N
274
N
C
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
N
N
286
S
C
N
287
N
C
N
288
N
O
N
289
N
C
Y
290
N
C
Y
291
N
C
Y
292
N
C
Y
293
N
C
Y
294
N
C
Y
295
N
C
N
296
N
O
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
N
N
309
S
C
N
310
N
C
N
311
N
O
N
312
N
C
N
313
N
C
N
314
N
C
N
315
N
O
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
N
N
326
S
C
N
327
N
C
N
328
N
O
N
329
N
C
N
330
N
O
N
331
N
O
N
332
N
H
N
333
N
H
N
334
N
H
N
335
N
H
N
336
N
H
N
337
N
H
N
338
N
H
N
339
N
N
N
340
S
C
N
341
N
C
N
342
N
O
N
343
R
C
N
344
N
O
N
345
N
C
N
346
N
O
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
N
N
357
S
C
N
358
N
C
N
359
N
O
N
360
N
C
Y
361
N
C
Y
362
N
C
Y
363
N
C
Y
364
N
N
Y
365
N
C
Y
366
N
C
Y
367
N
C
Y
368
N
C
Y
369
N
C
N
370
N
O
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
N
H
N
380
N
H
N
381
N
H
N
382
N
H
N
383
N
N
N
384
S
C
N
385
N
C
N
386
N
O
N
387
N
C
Y
388
N
C
Y
389
N
C
Y
390
N
C
Y
391
N
C
Y
392
N
C
Y
393
N
C
N
394
N
O
N
395
N
O
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
N
N
408
S
C
N
409
N
C
N
410
N
O
N
411
N
C
N
412
N
C
N
413
N
C
N
414
N
O
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
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
doub
N
84
N
sing
N
85
N
sing
N
86
E
doub
N
87
N
sing
N
88
N
sing
N
89
N
sing
Y
90
N
doub
Y
91
N
sing
Y
92
N
sing
N
93
N
sing
Y
94
N
doub
N
95
N
sing
Y
96
N
sing
N
97
N
sing
Y
98
N
doub
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
doub
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
doub
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
doub
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
doub
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
doub
N
157
N
sing
N
158
N
sing
N
159
N
sing
N
160
N
sing
Y
161
N
sing
Y
162
N
doub
Y
163
N
doub
N
164
N
sing
Y
165
N
sing
N
166
N
sing
Y
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
doub
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
doub
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
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
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
doub
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
Y
282
N
doub
Y
283
N
sing
Y
284
N
sing
N
285
N
sing
Y
286
N
doub
N
287
N
sing
Y
288
N
doub
N
289
N
sing
Y
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
doub
N
301
N
sing
N
302
N
sing
N
303
N
sing
N
304
N
sing
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
N
309
N
sing
N
310
N
sing
N
311
N
sing
N
312
N
sing
N
313
N
sing
N
314
N
sing
N
315
N
sing
N
316
N
sing
N
317
N
doub
N
318
N
sing
N
319
N
sing
N
320
N
sing
N
321
N
sing
N
322
N
sing
N
323
N
sing
N
324
N
sing
N
325
N
sing
N
326
N
sing
N
327
N
sing
N
328
N
sing
N
329
N
sing
N
330
N
doub
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
sing
N
349
N
sing
N
350
N
sing
Y
351
N
doub
Y
352
N
sing
Y
353
N
sing
N
354
N
sing
Y
355
N
doub
Y
356
N
sing
Y
357
N
sing
N
358
N
sing
Y
359
N
sing
Y
360
N
doub
N
361
N
sing
Y
362
N
doub
N
363
N
sing
Y
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
doub
N
375
N
sing
N
376
N
sing
N
377
N
sing
N
378
N
sing
Y
379
N
doub
Y
380
N
sing
Y
381
N
sing
N
382
N
sing
Y
383
N
doub
N
384
N
sing
Y
385
N
doub
N
386
N
sing
Y
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
doub
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
DK
Acta Crystallogr.,Sect.D
ABCRE6
0766
0907-4449
58
585
590
10.1107/S0907444902001257
11914481
Structure of the photoactive yellow protein reconstituted with caffeic acid at 1.16 A resolution.
2002
10.2210/pdb1kou/pdb
pdb_00001kou
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
100
1
IMAGE PLATE
1999-01-15
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.08
1.0
X26C
NSLS
1.08
SYNCHROTRON
NSLS BEAMLINE X26C
13888.575
PHOTOACTIVE YELLOW PROTEIN
1
man
polymer
180.157
CAFFEIC ACID
1
syn
non-polymer
58.122
N-BUTANE
1
syn
non-polymer
18.015
water
135
nat
water
PYP
no
no
MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK
EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV
MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK
EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV
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
Halorhodospira
Escherichia
sample
PYP
1053
Halorhodospira halophila
562
Escherichia coli
M15
plasmid
PHISP
1
1.54
20.2
VAPOR DIFFUSION, HANGING DROP
6.5
PEGMME 2000, MES, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 290K
290
pdbx_unobs_or_zero_occ_atoms
software
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_unobs_or_zero_occ_atoms
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Advisory
Refinement description
Advisory
Data collection
Database references
Derived calculations
Refinement description
1
0
2002-04-03
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-11
1
4
2023-08-16
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_struct_conn.pdbx_leaving_atom_flag
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
Crystal Structure Of The P65 Crystal Form Of Photoactive Yellow Protein
RCSB
Y
RCSB
2001-12-22
REL
REL
DHC
CAFFEIC ACID
NBU
N-BUTANE
HOH
water
2PHY
PDB ENTRY 2PHY
PDB
experimental model
CAF
201
2
DHC
DHC
201
A
C4
205
3
NBU
NBU
205
A
HOH
1001
4
HOH
HOH
1001
A
HOH
1002
4
HOH
HOH
1002
A
HOH
1003
4
HOH
HOH
1003
A
HOH
1004
4
HOH
HOH
1004
A
HOH
1005
4
HOH
HOH
1005
A
HOH
1006
4
HOH
HOH
1006
A
HOH
1007
4
HOH
HOH
1007
A
HOH
1008
4
HOH
HOH
1008
A
HOH
1009
4
HOH
HOH
1009
A
HOH
1010
4
HOH
HOH
1010
A
HOH
1011
4
HOH
HOH
1011
A
HOH
1012
4
HOH
HOH
1012
A
HOH
1013
4
HOH
HOH
1013
A
HOH
1014
4
HOH
HOH
1014
A
HOH
1015
4
HOH
HOH
1015
A
HOH
1016
4
HOH
HOH
1016
A
HOH
1017
4
HOH
HOH
1017
A
HOH
1018
4
HOH
HOH
1018
A
HOH
1019
4
HOH
HOH
1019
A
HOH
1020
4
HOH
HOH
1020
A
HOH
1021
4
HOH
HOH
1021
A
HOH
1022
4
HOH
HOH
1022
A
HOH
1023
4
HOH
HOH
1023
A
HOH
1024
4
HOH
HOH
1024
A
HOH
1025
4
HOH
HOH
1025
A
HOH
1026
4
HOH
HOH
1026
A
HOH
1027
4
HOH
HOH
1027
A
HOH
1028
4
HOH
HOH
1028
A
HOH
1029
4
HOH
HOH
1029
A
HOH
1030
4
HOH
HOH
1030
A
HOH
1031
4
HOH
HOH
1031
A
HOH
1032
4
HOH
HOH
1032
A
HOH
1033
4
HOH
HOH
1033
A
HOH
1034
4
HOH
HOH
1034
A
HOH
1035
4
HOH
HOH
1035
A
HOH
1036
4
HOH
HOH
1036
A
HOH
1037
4
HOH
HOH
1037
A
HOH
1038
4
HOH
HOH
1038
A
HOH
1039
4
HOH
HOH
1039
A
HOH
1040
4
HOH
HOH
1040
A
HOH
1041
4
HOH
HOH
1041
A
HOH
1042
4
HOH
HOH
1042
A
HOH
1043
4
HOH
HOH
1043
A
HOH
1044
4
HOH
HOH
1044
A
HOH
1045
4
HOH
HOH
1045
A
HOH
1046
4
HOH
HOH
1046
A
HOH
1047
4
HOH
HOH
1047
A
HOH
1048
4
HOH
HOH
1048
A
HOH
1049
4
HOH
HOH
1049
A
HOH
1050
4
HOH
HOH
1050
A
HOH
1051
4
HOH
HOH
1051
A
HOH
1052
4
HOH
HOH
1052
A
HOH
1053
4
HOH
HOH
1053
A
HOH
1054
4
HOH
HOH
1054
A
HOH
1055
4
HOH
HOH
1055
A
HOH
1056
4
HOH
HOH
1056
A
HOH
1057
4
HOH
HOH
1057
A
HOH
1058
4
HOH
HOH
1058
A
HOH
1059
4
HOH
HOH
1059
A
HOH
1060
4
HOH
HOH
1060
A
HOH
1061
4
HOH
HOH
1061
A
HOH
1062
4
HOH
HOH
1062
A
HOH
1063
4
HOH
HOH
1063
A
HOH
1064
4
HOH
HOH
1064
A
HOH
1065
4
HOH
HOH
1065
A
HOH
1066
4
HOH
HOH
1066
A
HOH
1067
4
HOH
HOH
1067
A
HOH
1068
4
HOH
HOH
1068
A
HOH
1069
4
HOH
HOH
1069
A
HOH
1070
4
HOH
HOH
1070
A
HOH
1071
4
HOH
HOH
1071
A
HOH
1072
4
HOH
HOH
1072
A
HOH
1073
4
HOH
HOH
1073
A
HOH
1074
4
HOH
HOH
1074
A
HOH
1075
4
HOH
HOH
1075
A
HOH
1076
4
HOH
HOH
1076
A
HOH
1077
4
HOH
HOH
1077
A
HOH
1078
4
HOH
HOH
1078
A
HOH
1079
4
HOH
HOH
1079
A
HOH
1080
4
HOH
HOH
1080
A
HOH
1081
4
HOH
HOH
1081
A
HOH
1082
4
HOH
HOH
1082
A
HOH
1083
4
HOH
HOH
1083
A
HOH
1084
4
HOH
HOH
1084
A
HOH
1085
4
HOH
HOH
1085
A
HOH
1086
4
HOH
HOH
1086
A
HOH
1087
4
HOH
HOH
1087
A
HOH
1088
4
HOH
HOH
1088
A
HOH
1089
4
HOH
HOH
1089
A
HOH
1090
4
HOH
HOH
1090
A
HOH
1091
4
HOH
HOH
1091
A
HOH
1092
4
HOH
HOH
1092
A
HOH
1093
4
HOH
HOH
1093
A
HOH
1094
4
HOH
HOH
1094
A
HOH
1095
4
HOH
HOH
1095
A
HOH
1096
4
HOH
HOH
1096
A
HOH
1097
4
HOH
HOH
1097
A
HOH
1098
4
HOH
HOH
1098
A
HOH
1099
4
HOH
HOH
1099
A
HOH
1100
4
HOH
HOH
1100
A
HOH
1101
4
HOH
HOH
1101
A
HOH
1102
4
HOH
HOH
1102
A
HOH
1103
4
HOH
HOH
1103
A
HOH
1104
4
HOH
HOH
1104
A
HOH
1105
4
HOH
HOH
1105
A
HOH
1106
4
HOH
HOH
1106
A
HOH
1107
4
HOH
HOH
1107
A
HOH
1108
4
HOH
HOH
1108
A
HOH
1109
4
HOH
HOH
1109
A
HOH
1110
4
HOH
HOH
1110
A
HOH
1111
4
HOH
HOH
1111
A
HOH
1112
4
HOH
HOH
1112
A
HOH
1113
4
HOH
HOH
1113
A
HOH
1114
4
HOH
HOH
1114
A
HOH
1115
4
HOH
HOH
1115
A
HOH
1116
4
HOH
HOH
1116
A
HOH
1117
4
HOH
HOH
1117
A
HOH
1118
4
HOH
HOH
1118
A
HOH
1119
4
HOH
HOH
1119
A
HOH
1120
4
HOH
HOH
1120
A
HOH
1121
4
HOH
HOH
1121
A
HOH
1122
4
HOH
HOH
1122
A
HOH
1123
4
HOH
HOH
1123
A
HOH
1124
4
HOH
HOH
1124
A
HOH
1125
4
HOH
HOH
1125
A
HOH
1126
4
HOH
HOH
1126
A
HOH
1127
4
HOH
HOH
1127
A
HOH
1128
4
HOH
HOH
1128
A
HOH
1129
4
HOH
HOH
1129
A
HOH
1130
4
HOH
HOH
1130
A
HOH
1131
4
HOH
HOH
1131
A
HOH
1132
4
HOH
HOH
1132
A
HOH
1133
4
HOH
HOH
1133
A
HOH
1134
4
HOH
HOH
1134
A
HOH
1135
4
HOH
HOH
1135
A
n
1
1
A
n
2
2
A
n
3
3
A
VAL
4
n
4
VAL
4
A
ALA
5
n
5
ALA
5
A
PHE
6
n
6
PHE
6
A
GLY
7
n
7
GLY
7
A
SER
8
n
8
SER
8
A
GLU
9
n
9
GLU
9
A
ASP
10
n
10
ASP
10
A
ILE
11
n
11
ILE
11
A
GLU
12
n
12
GLU
12
A
ASN
13
n
13
ASN
13
A
THR
14
n
14
THR
14
A
LEU
15
n
15
LEU
15
A
ALA
16
n
16
ALA
16
A
LYS
17
n
17
LYS
17
A
MET
18
n
18
MET
18
A
ASP
19
n
19
ASP
19
A
ASP
20
n
20
ASP
20
A
GLY
21
n
21
GLY
21
A
GLN
22
n
22
GLN
22
A
LEU
23
n
23
LEU
23
A
ASP
24
n
24
ASP
24
A
GLY
25
n
25
GLY
25
A
LEU
26
n
26
LEU
26
A
ALA
27
n
27
ALA
27
A
PHE
28
n
28
PHE
28
A
GLY
29
n
29
GLY
29
A
ALA
30
n
30
ALA
30
A
ILE
31
n
31
ILE
31
A
GLN
32
n
32
GLN
32
A
LEU
33
n
33
LEU
33
A
ASP
34
n
34
ASP
34
A
GLY
35
n
35
GLY
35
A
ASP
36
n
36
ASP
36
A
GLY
37
n
37
GLY
37
A
ASN
38
n
38
ASN
38
A
ILE
39
n
39
ILE
39
A
LEU
40
n
40
LEU
40
A
GLN
41
n
41
GLN
41
A
TYR
42
n
42
TYR
42
A
ASN
43
n
43
ASN
43
A
ALA
44
n
44
ALA
44
A
ALA
45
n
45
ALA
45
A
GLU
46
n
46
GLU
46
A
GLY
47
n
47
GLY
47
A
ASP
48
n
48
ASP
48
A
ILE
49
n
49
ILE
49
A
THR
50
n
50
THR
50
A
GLY
51
n
51
GLY
51
A
ARG
52
n
52
ARG
52
A
ASP
53
n
53
ASP
53
A
PRO
54
n
54
PRO
54
A
LYS
55
n
55
LYS
55
A
GLN
56
n
56
GLN
56
A
VAL
57
n
57
VAL
57
A
ILE
58
n
58
ILE
58
A
GLY
59
n
59
GLY
59
A
LYS
60
n
60
LYS
60
A
ASN
61
n
61
ASN
61
A
PHE
62
n
62
PHE
62
A
PHE
63
n
63
PHE
63
A
LYS
64
n
64
LYS
64
A
ASP
65
n
65
ASP
65
A
VAL
66
n
66
VAL
66
A
ALA
67
n
67
ALA
67
A
PRO
68
n
68
PRO
68
A
CYS
69
n
69
CYS
69
A
THR
70
n
70
THR
70
A
ASP
71
n
71
ASP
71
A
SER
72
n
72
SER
72
A
PRO
73
n
73
PRO
73
A
GLU
74
n
74
GLU
74
A
PHE
75
n
75
PHE
75
A
TYR
76
n
76
TYR
76
A
GLY
77
n
77
GLY
77
A
LYS
78
n
78
LYS
78
A
PHE
79
n
79
PHE
79
A
LYS
80
n
80
LYS
80
A
GLU
81
n
81
GLU
81
A
GLY
82
n
82
GLY
82
A
VAL
83
n
83
VAL
83
A
ALA
84
n
84
ALA
84
A
SER
85
n
85
SER
85
A
GLY
86
n
86
GLY
86
A
ASN
87
n
87
ASN
87
A
LEU
88
n
88
LEU
88
A
ASN
89
n
89
ASN
89
A
THR
90
n
90
THR
90
A
MET
91
n
91
MET
91
A
PHE
92
n
92
PHE
92
A
GLU
93
n
93
GLU
93
A
TYR
94
n
94
TYR
94
A
THR
95
n
95
THR
95
A
PHE
96
n
96
PHE
96
A
ASP
97
n
97
ASP
97
A
TYR
98
n
98
TYR
98
A
GLN
99
n
99
GLN
99
A
MET
100
n
100
MET
100
A
THR
101
n
101
THR
101
A
PRO
102
n
102
PRO
102
A
THR
103
n
103
THR
103
A
LYS
104
n
104
LYS
104
A
VAL
105
n
105
VAL
105
A
LYS
106
n
106
LYS
106
A
VAL
107
n
107
VAL
107
A
HIS
108
n
108
HIS
108
A
MET
109
n
109
MET
109
A
LYS
110
n
110
LYS
110
A
LYS
111
n
111
LYS
111
A
ALA
112
n
112
ALA
112
A
LEU
113
n
113
LEU
113
A
n
114
114
A
n
115
115
A
ASP
116
n
116
ASP
116
A
SER
117
n
117
SER
117
A
TYR
118
n
118
TYR
118
A
TRP
119
n
119
TRP
119
A
VAL
120
n
120
VAL
120
A
PHE
121
n
121
PHE
121
A
VAL
122
n
122
VAL
122
A
LYS
123
n
123
LYS
123
A
ARG
124
n
124
ARG
124
A
VAL
125
n
125
VAL
125
A
0.1471000
0.1621000
0.1468000
0.1618000
0.1845000
0.2026000
1397
1736
5.0
5.0
27674
author_defined_assembly
1
monomeric
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
LEU
40
A
O
LEU
40
A
N
GLN
32
A
N
GLN
32
A
N
LEU
33
A
N
LEU
33
A
O
TYR
118
A
O
TYR
118
A
O
TRP
119
A
O
TRP
119
A
N
LYS
110
A
N
LYS
110
A
O
VAL
107
A
O
VAL
107
A
N
PHE
92
A
N
PHE
92
1
A
CG
GLU
9
A
CG
GLU
9
0
Y
1
A
CD
GLU
9
A
CD
GLU
9
0
Y
1
A
OE1
GLU
9
A
OE1
GLU
9
0
Y
1
A
OE2
GLU
9
A
OE2
GLU
9
0
Y
1
A
CD
LYS
55
A
CD
LYS
55
0
Y
1
A
CE
LYS
55
A
CE
LYS
55
0
Y
1
A
NZ
LYS
55
A
NZ
LYS
55
0
Y
1
A
CE
LYS
60
A
CE
LYS
60
0
Y
1
A
NZ
LYS
60
A
NZ
LYS
60
0
Y
1
A
CD
LYS
104
A
CD
LYS
104
0
Y
1
A
CE
LYS
104
A
CE
LYS
104
0
Y
1
A
NZ
LYS
104
A
NZ
LYS
104
0
Y
1
A
CD
LYS
111
A
CD
LYS
111
0
Y
1
A
CE
LYS
111
A
CE
LYS
111
0
Y
1
A
NZ
LYS
111
A
NZ
LYS
111
0
Y
1
A
N
ASP
116
A
N
ASP
116
1
Y
1
A
CA
ASP
116
A
CA
ASP
116
1
Y
1
A
CB
ASP
116
A
CB
ASP
116
1
Y
1
A
CG
ASP
116
A
CG
ASP
116
1
Y
1
A
OD1
ASP
116
A
OD1
ASP
116
1
Y
1
A
OD2
ASP
116
A
OD2
ASP
116
1
Y
1
A
MET
1
A
MET
1
1
Y
1
A
GLU
2
A
GLU
2
1
Y
1
A
HIS
3
A
HIS
3
1
Y
1
A
SER
114
A
SER
114
1
Y
1
A
GLY
115
A
GLY
115
1
Y
1
A
A
OE1
O
GLU
HOH
9
1079
2.01
1
A
SER
117
10.92
1
-3.70
0.60
121.00
117.30
A
A
A
CB
CG
CD2
TYR
TYR
TYR
76
76
76
N
1
3.70
0.60
121.00
124.70
A
A
A
CB
CG
CD1
TYR
TYR
TYR
76
76
76
N
1
12.05
1.70
113.30
125.35
A
A
A
CA
CB
CG
MET
MET
MET
91
91
91
N
1
3.54
0.50
120.30
123.84
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
124
124
124
N
1
-5.30
0.50
120.30
115.00
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
124
124
124
N
1
A
PHE
75
-127.78
-81.22
1
A
ASN
89
-166.17
90.42
1
A
ASP
97
-146.72
17.92
20.24
0.2026000
0.1618000
0.1621000
1.16
8.00
9856
1736
34756
12084
5.0
92.3
RANDOM
1
FREE R
0.0
MOLECULAR REPLACEMENT
PDB ENTRY 2PHY
ENGH & HUBER
0.1
5
862.00
1069.00
1.16
8.00
135
1102
24
0
943
0.009
0.026
0.000
0.0338
0.140
0.124
0.028
0.005
0.054
0.096
1.16
15.0
1KOU
36609
-3.0
0.0400000
1
15.7
9.1
96.7
0.5460000
1.16
1.20
2.7
3352
89.4
phasing
AMoRE
refinement
SHELXL-97
data reduction
DENZO
data scaling
SCALEPACK
Crystal Structure of the Photoactive Yellow Protein Reconstituted with Caffeic Acid at 1.16 A Resolution
1
N
N
2
N
N
3
N
N
4
N
N
A
ASP
10
A
ASP
10
HELX_P
A
LYS
17
A
LYS
17
1
1
8
A
ASP
19
A
ASP
19
HELX_P
A
GLY
25
A
GLY
25
1
2
7
A
ASN
43
A
ASN
43
HELX_P
A
GLY
51
A
GLY
51
1
3
9
A
ASP
53
A
ASP
53
HELX_P
A
ILE
58
A
ILE
58
1
4
6
A
ALA
67
A
ALA
67
HELX_P
A
ASP
71
A
ASP
71
5
5
5
A
PHE
75
A
PHE
75
HELX_P
A
GLY
86
A
GLY
86
1
6
12
covale
1.781
none
A
CYS
69
A
SG
CYS
69
1_555
A
DHC
201
B
C1
DHC
1_555
PHOTOSYNTHESIS
photoreceptor, PHOTOSYNTHESIS
PYP_ECTHA
UNP
1
1
P16113
MEHVAFGSEDIENTLAKMDDGQLDGLAFGAIQLDGDGNILQYNAAEGDITGRDPKQVIGKNFFKDVAPCTDSPEFYGKFK
EGVASGNLNTMFEYTFDYQMTPTKVKVHMKKALSGDSYWVFVKRV
1
125
1KOU
1
125
P16113
A
1
1
125
5
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ILE
39
A
ILE
39
A
TYR
42
A
TYR
42
A
GLY
29
A
GLY
29
A
LEU
33
A
LEU
33
A
TYR
118
A
TYR
118
A
ARG
124
A
ARG
124
A
THR
103
A
THR
103
A
LYS
111
A
LYS
111
A
ASN
89
A
ASN
89
A
PHE
96
A
PHE
96
BINDING SITE FOR RESIDUE DHC A 201
A
DHC
201
Software
12
BINDING SITE FOR RESIDUE NBU A 205
A
NBU
205
Software
8
A
ILE
31
A
ILE
31
12
1_555
A
TYR
42
A
TYR
42
12
1_555
A
GLU
46
A
GLU
46
12
1_555
A
THR
50
A
THR
50
12
1_555
A
ARG
52
A
ARG
52
12
1_555
A
PHE
62
A
PHE
62
12
1_555
A
VAL
66
A
VAL
66
12
1_555
A
ALA
67
A
ALA
67
12
1_555
A
PRO
68
A
PRO
68
12
1_555
A
CYS
69
A
CYS
69
12
1_555
A
PHE
96
A
PHE
96
12
1_555
A
TYR
98
A
TYR
98
12
1_555
A
ASN
38
A
ASN
38
8
5_565
A
GLY
59
A
GLY
59
8
5_565
A
GLU
81
A
GLU
81
8
1_555
A
GLY
82
A
GLY
82
8
1_555
A
SER
85
A
SER
85
8
1_555
A
ASN
87
A
ASN
87
8
1_555
A
HOH
1041
D
HOH
8
1_555
A
HOH
1065
D
HOH
8
5_565
170
P 65