0.0160450
0.0092630
0.0000000
0.0000000
0.0185270
0.0000000
0.0000000
0.0000000
0.0109620
0.0000000
0.0000000
0.0000000
Esters, H.
Scheidig, A.J.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
6
90.00
90.00
120.00
62.326
62.326
91.221
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
C10 H15 N5 O11 P2
443.201
n
GUANOSINE-5'-DIPHOSPHATE
RNA 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
C10 H17 N6 O13 P3
522.196
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
non-polymer
C6 H10 N3 O2 1
156.162
y
HISTIDINE
L-peptide linking
H2 O
18.015
WATER
non-polymer
C6 H13 N O2
131.173
y
ISOLEUCINE
L-peptide linking
C6 H13 N O2
131.173
y
LEUCINE
L-peptide linking
C6 H15 N2 O2 1
147.195
y
LYSINE
L-peptide linking
C5 H11 N O2 S
149.211
y
METHIONINE
L-peptide linking
Mg 2
24.305
MAGNESIUM ION
non-polymer
C5 H11 N O3 S
165.211
n
S-OXYMETHIONINE
L-peptide linking
Ni 2
58.693
NICKEL (II) ION
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
P
N
75
N
O
N
76
N
O
N
77
N
O
N
78
N
O
N
79
N
P
N
80
N
O
N
81
N
O
N
82
N
O
N
83
N
C
N
84
R
C
N
85
N
O
N
86
S
C
N
87
N
O
N
88
R
C
N
89
N
O
N
90
R
C
Y
91
N
N
Y
92
N
C
Y
93
N
N
Y
94
N
C
N
95
N
C
N
96
N
O
N
97
N
N
N
98
N
C
N
99
N
N
N
100
N
N
Y
101
N
C
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
N
N
118
S
C
N
119
N
C
N
120
N
O
N
121
N
C
N
122
N
C
N
123
N
C
N
124
N
O
N
125
N
N
N
126
N
O
N
127
N
H
N
128
N
H
N
129
N
H
N
130
N
H
N
131
N
H
N
132
N
H
N
133
N
H
N
134
N
H
N
135
N
H
N
136
N
H
N
137
N
N
N
138
S
C
N
139
N
C
N
140
N
O
N
141
N
C
N
142
N
C
N
143
N
C
N
144
N
O
N
145
N
O
N
146
N
O
N
147
N
H
N
148
N
H
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
N
N
157
N
C
N
158
N
C
N
159
N
O
N
160
N
O
N
161
N
H
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
P
N
167
N
O
N
168
N
O
N
169
N
O
N
170
N
N
N
171
R
P
N
172
N
O
N
173
N
O
N
174
N
O
N
175
S
P
N
176
N
O
N
177
N
O
N
178
N
O
N
179
N
C
N
180
R
C
N
181
N
O
N
182
S
C
N
183
N
O
N
184
R
C
N
185
N
O
N
186
R
C
Y
187
N
N
Y
188
N
C
Y
189
N
N
Y
190
N
C
Y
191
N
C
N
192
N
O
Y
193
N
N
Y
194
N
C
N
195
N
N
Y
196
N
N
Y
197
N
C
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
H
N
210
N
H
N
211
N
H
N
212
N
H
N
213
N
H
N
214
N
H
N
215
N
N
N
216
S
C
N
217
N
C
N
218
N
O
N
219
N
C
Y
220
N
C
Y
221
N
N
Y
222
N
C
Y
223
N
C
Y
224
N
N
N
225
N
O
N
226
N
H
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
O
N
237
N
H
N
238
N
H
N
239
N
N
N
240
S
C
N
241
N
C
N
242
N
O
N
243
S
C
N
244
N
C
N
245
N
C
N
246
N
C
N
247
N
O
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
N
N
262
S
C
N
263
N
C
N
264
N
O
N
265
N
C
N
266
N
C
N
267
N
C
N
268
N
C
N
269
N
O
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
N
N
284
S
C
N
285
N
C
N
286
N
O
N
287
N
C
N
288
N
C
N
289
N
C
N
290
N
C
N
291
N
N
N
292
N
O
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
N
N
309
S
C
N
310
N
C
N
311
N
O
N
312
N
C
N
313
N
C
N
314
N
S
N
315
N
C
N
316
N
O
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
MG
N
329
N
N
N
330
S
C
N
331
N
C
N
332
N
C
N
333
S
S
N
334
N
C
N
335
N
C
N
336
N
O
N
337
N
O
N
338
N
O
N
339
N
H
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
H
N
350
N
NI
N
351
N
N
N
352
S
C
N
353
N
C
N
354
N
O
N
355
N
C
Y
356
N
C
Y
357
N
C
Y
358
N
C
Y
359
N
C
Y
360
N
C
Y
361
N
C
N
362
N
O
N
363
N
H
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
N
N
375
S
C
N
376
N
C
N
377
N
O
N
378
N
C
N
379
N
C
N
380
N
C
N
381
N
O
N
382
N
H
N
383
N
H
N
384
N
H
N
385
N
H
N
386
N
H
N
387
N
H
N
388
N
H
N
389
N
H
N
390
N
H
N
391
N
N
N
392
S
C
N
393
N
C
N
394
N
O
N
395
N
C
N
396
N
O
N
397
N
O
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
N
N
406
S
C
N
407
N
C
N
408
N
O
N
409
R
C
N
410
N
O
N
411
N
C
N
412
N
O
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
N
N
423
S
C
N
424
N
C
N
425
N
O
N
426
N
C
Y
427
N
C
Y
428
N
C
Y
429
N
C
Y
430
N
N
Y
431
N
C
Y
432
N
C
Y
433
N
C
Y
434
N
C
Y
435
N
C
N
436
N
O
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
N
N
450
S
C
N
451
N
C
N
452
N
O
N
453
N
C
Y
454
N
C
Y
455
N
C
Y
456
N
C
Y
457
N
C
Y
458
N
C
Y
459
N
C
N
460
N
O
N
461
N
O
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
N
N
474
S
C
N
475
N
C
N
476
N
O
N
477
N
C
N
478
N
C
N
479
N
C
N
480
N
O
N
481
N
H
N
482
N
H
N
483
N
H
N
484
N
H
N
485
N
H
N
486
N
H
N
487
N
H
N
488
N
H
N
489
N
H
N
490
N
H
N
491
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
doub
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
doub
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
Y
99
N
sing
Y
100
N
sing
Y
101
N
doub
N
102
N
sing
Y
103
N
sing
N
104
N
sing
Y
105
N
doub
N
106
N
doub
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
doub
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
doub
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
sing
N
138
N
sing
N
139
N
sing
N
140
N
doub
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
doub
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
doub
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
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
Y
196
N
sing
Y
197
N
sing
Y
198
N
doub
N
199
N
sing
Y
200
N
sing
Y
201
N
sing
Y
202
N
doub
N
203
N
doub
Y
204
N
sing
Y
205
N
sing
N
206
N
sing
N
207
N
sing
Y
208
N
doub
N
209
N
sing
N
210
N
sing
Y
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
Y
223
N
sing
Y
224
N
doub
Y
225
N
doub
N
226
N
sing
Y
227
N
sing
N
228
N
sing
Y
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
doub
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
doub
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
doub
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
doub
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
doub
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
doub
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
N
356
N
sing
Y
357
N
doub
N
358
N
sing
Y
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
doub
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
doub
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
doub
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
doub
N
416
N
sing
N
417
N
sing
N
418
N
sing
N
419
N
sing
Y
420
N
doub
Y
421
N
sing
Y
422
N
sing
N
423
N
sing
Y
424
N
doub
Y
425
N
sing
Y
426
N
sing
N
427
N
sing
Y
428
N
sing
Y
429
N
doub
N
430
N
sing
Y
431
N
doub
N
432
N
sing
Y
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
doub
N
444
N
sing
N
445
N
sing
N
446
N
sing
N
447
N
sing
Y
448
N
doub
Y
449
N
sing
Y
450
N
sing
N
451
N
sing
Y
452
N
doub
N
453
N
sing
Y
454
N
doub
N
455
N
sing
Y
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
doub
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
sing
UK
J.Mol.Biol.
JMOBAK
0070
0022-2836
298
111
121
10.1006/jmbi.2000.3645
10756108
High-resolution crystal structure of S. cerevisiae Ypt51(DeltaC15)-GppNHp, a small GTP-binding protein involved in regulation of endocytosis.
2000
10.2210/pdb1ek0/pdb
pdb_00001ek0
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
MIRROR
IMAGE PLATE
1999-06-01
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
0.903
1.0
X11
EMBL/DESY, HAMBURG
0.903
SYNCHROTRON
EMBL/DESY, HAMBURG BEAMLINE X11
18963.666
PROTEIN (GTP-BINDING PROTEIN YPT51)
GTPASE DOMAIN
1
man
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
58.693
NICKEL (II) ION
1
syn
non-polymer
522.196
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
1
syn
non-polymer
443.201
GUANOSINE-5'-DIPHOSPHATE
1
syn
non-polymer
18.015
water
209
nat
water
no
yes
VTSIKLVLLGEAAVGKSSIVLRFVSNDFAENKEPTIGAAFLTQRVTINEHTVKFEIWDTAGQERFASLAP(MHO)YYRNA
QAALVVYDVTKPQSFIKARHWVKELHEQASKDIIIALVGNKID(MHO)LQEGGERKVAREEGEKLAEEKGLLFFETSAKT
GENVNDVFLGIGEKIPLK
VTSIKLVLLGEAAVGKSSIVLRFVSNDFAENKEPTIGAAFLTQRVTINEHTVKFEIWDTAGQERFASLAPMYYRNAQAAL
VVYDVTKPQSFIKARHWVKELHEQASKDIIIALVGNKIDMLQEGGERKVAREEGEKLAEEKGLLFFETSAKTGENVNDVF
LGIGEKIPLK
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
baker's yeast
Saccharomyces
Escherichia
Escherichia coli
sample
4932
Saccharomyces cerevisiae
469008
Escherichia coli BL21(DE3)
BL21/DE3
PET19
1
2
54.38
VAPOR DIFFUSION, HANGING DROP
7.5
10% PEG-3350,
100 MM HEPES, PH 7.5,
20 MM NICL2 , VAPOR DIFFUSION, HANGING DROP, temperature 291K
291
software
chem_comp_atom
chem_comp_bond
database_2
diffrn_source
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Version format compliance
Version format compliance
Refinement description
Data collection
Database references
Derived calculations
Refinement description
1
0
2000-04-17
1
1
2008-04-27
1
2
2011-07-13
1
3
2017-10-04
1
4
2023-08-09
_software.classification
_software.name
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_diffrn_source.pdbx_synchrotron_site
_pdbx_struct_conn_angle.ptnr1_auth_comp_id
_pdbx_struct_conn_angle.ptnr1_auth_seq_id
_pdbx_struct_conn_angle.ptnr1_label_asym_id
_pdbx_struct_conn_angle.ptnr1_label_atom_id
_pdbx_struct_conn_angle.ptnr1_label_comp_id
_pdbx_struct_conn_angle.ptnr1_label_seq_id
_pdbx_struct_conn_angle.ptnr3_auth_comp_id
_pdbx_struct_conn_angle.ptnr3_auth_seq_id
_pdbx_struct_conn_angle.ptnr3_label_asym_id
_pdbx_struct_conn_angle.ptnr3_label_atom_id
_pdbx_struct_conn_angle.ptnr3_label_comp_id
_pdbx_struct_conn_angle.ptnr3_label_seq_id
_pdbx_struct_conn_angle.value
_struct_conn.pdbx_dist_value
_struct_conn.pdbx_leaving_atom_flag
_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_comp_id
_struct_conn.ptnr2_auth_seq_id
_struct_conn.ptnr2_label_asym_id
_struct_conn.ptnr2_label_atom_id
_struct_conn.ptnr2_label_comp_id
_struct_conn.ptnr2_label_seq_id
_struct_ref_seq_dif.details
_struct_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
RCSB
Y
RCSB
2000-03-06
REL
REL
MG
MAGNESIUM ION
NI
NICKEL (II) ION
GNP
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
GDP
GUANOSINE-5'-DIPHOSPHATE
HOH
water
5P21
PDB
experimental model
MG
601
2
MG
MG
601
A
NI
602
3
NI
NI
602
A
GNP
501
4
GNP
GNP
501
A
GDP
502
5
GDP
GDP
502
A
HOH
1001
6
HOH
HOH
1001
A
HOH
1002
6
HOH
HOH
1002
A
HOH
1003
6
HOH
HOH
1003
A
HOH
1004
6
HOH
HOH
1004
A
HOH
1005
6
HOH
HOH
1005
A
HOH
1006
6
HOH
HOH
1006
A
HOH
1007
6
HOH
HOH
1007
A
HOH
1008
6
HOH
HOH
1008
A
HOH
1009
6
HOH
HOH
1009
A
HOH
1010
6
HOH
HOH
1010
A
HOH
1011
6
HOH
HOH
1011
A
HOH
1012
6
HOH
HOH
1012
A
HOH
1013
6
HOH
HOH
1013
A
HOH
1014
6
HOH
HOH
1014
A
HOH
1015
6
HOH
HOH
1015
A
HOH
1016
6
HOH
HOH
1016
A
HOH
1017
6
HOH
HOH
1017
A
HOH
1018
6
HOH
HOH
1018
A
HOH
1019
6
HOH
HOH
1019
A
HOH
1020
6
HOH
HOH
1020
A
HOH
1021
6
HOH
HOH
1021
A
HOH
1022
6
HOH
HOH
1022
A
HOH
1023
6
HOH
HOH
1023
A
HOH
1024
6
HOH
HOH
1024
A
HOH
1025
6
HOH
HOH
1025
A
HOH
1026
6
HOH
HOH
1026
A
HOH
1027
6
HOH
HOH
1027
A
HOH
1028
6
HOH
HOH
1028
A
HOH
1029
6
HOH
HOH
1029
A
HOH
1030
6
HOH
HOH
1030
A
HOH
1031
6
HOH
HOH
1031
A
HOH
1032
6
HOH
HOH
1032
A
HOH
1033
6
HOH
HOH
1033
A
HOH
1034
6
HOH
HOH
1034
A
HOH
1035
6
HOH
HOH
1035
A
HOH
1036
6
HOH
HOH
1036
A
HOH
1037
6
HOH
HOH
1037
A
HOH
1038
6
HOH
HOH
1038
A
HOH
1039
6
HOH
HOH
1039
A
HOH
1040
6
HOH
HOH
1040
A
HOH
1041
6
HOH
HOH
1041
A
HOH
1042
6
HOH
HOH
1042
A
HOH
1043
6
HOH
HOH
1043
A
HOH
1044
6
HOH
HOH
1044
A
HOH
1045
6
HOH
HOH
1045
A
HOH
1046
6
HOH
HOH
1046
A
HOH
1047
6
HOH
HOH
1047
A
HOH
1048
6
HOH
HOH
1048
A
HOH
1049
6
HOH
HOH
1049
A
HOH
1050
6
HOH
HOH
1050
A
HOH
1051
6
HOH
HOH
1051
A
HOH
1052
6
HOH
HOH
1052
A
HOH
1053
6
HOH
HOH
1053
A
HOH
1054
6
HOH
HOH
1054
A
HOH
1055
6
HOH
HOH
1055
A
HOH
1056
6
HOH
HOH
1056
A
HOH
1057
6
HOH
HOH
1057
A
HOH
1058
6
HOH
HOH
1058
A
HOH
1059
6
HOH
HOH
1059
A
HOH
1060
6
HOH
HOH
1060
A
HOH
1061
6
HOH
HOH
1061
A
HOH
1062
6
HOH
HOH
1062
A
HOH
1063
6
HOH
HOH
1063
A
HOH
1064
6
HOH
HOH
1064
A
HOH
1065
6
HOH
HOH
1065
A
HOH
1066
6
HOH
HOH
1066
A
HOH
1067
6
HOH
HOH
1067
A
HOH
1068
6
HOH
HOH
1068
A
HOH
1069
6
HOH
HOH
1069
A
HOH
1070
6
HOH
HOH
1070
A
HOH
1071
6
HOH
HOH
1071
A
HOH
1072
6
HOH
HOH
1072
A
HOH
1073
6
HOH
HOH
1073
A
HOH
1074
6
HOH
HOH
1074
A
HOH
1075
6
HOH
HOH
1075
A
HOH
1076
6
HOH
HOH
1076
A
HOH
1077
6
HOH
HOH
1077
A
HOH
1078
6
HOH
HOH
1078
A
HOH
1079
6
HOH
HOH
1079
A
HOH
1080
6
HOH
HOH
1080
A
HOH
1081
6
HOH
HOH
1081
A
HOH
1082
6
HOH
HOH
1082
A
HOH
1083
6
HOH
HOH
1083
A
HOH
1084
6
HOH
HOH
1084
A
HOH
1085
6
HOH
HOH
1085
A
HOH
1086
6
HOH
HOH
1086
A
HOH
1087
6
HOH
HOH
1087
A
HOH
1088
6
HOH
HOH
1088
A
HOH
1089
6
HOH
HOH
1089
A
HOH
1090
6
HOH
HOH
1090
A
HOH
1091
6
HOH
HOH
1091
A
HOH
1092
6
HOH
HOH
1092
A
HOH
1093
6
HOH
HOH
1093
A
HOH
1094
6
HOH
HOH
1094
A
HOH
1095
6
HOH
HOH
1095
A
HOH
1096
6
HOH
HOH
1096
A
HOH
1097
6
HOH
HOH
1097
A
HOH
1098
6
HOH
HOH
1098
A
HOH
1099
6
HOH
HOH
1099
A
HOH
1100
6
HOH
HOH
1100
A
HOH
1101
6
HOH
HOH
1101
A
HOH
1102
6
HOH
HOH
1102
A
HOH
1103
6
HOH
HOH
1103
A
HOH
1104
6
HOH
HOH
1104
A
HOH
1105
6
HOH
HOH
1105
A
HOH
1106
6
HOH
HOH
1106
A
HOH
1107
6
HOH
HOH
1107
A
HOH
1108
6
HOH
HOH
1108
A
HOH
1109
6
HOH
HOH
1109
A
HOH
1110
6
HOH
HOH
1110
A
HOH
1111
6
HOH
HOH
1111
A
HOH
1112
6
HOH
HOH
1112
A
HOH
1113
6
HOH
HOH
1113
A
HOH
1114
6
HOH
HOH
1114
A
HOH
1115
6
HOH
HOH
1115
A
HOH
1116
6
HOH
HOH
1116
A
HOH
1117
6
HOH
HOH
1117
A
HOH
1118
6
HOH
HOH
1118
A
HOH
1119
6
HOH
HOH
1119
A
HOH
1120
6
HOH
HOH
1120
A
HOH
1121
6
HOH
HOH
1121
A
HOH
1122
6
HOH
HOH
1122
A
HOH
1123
6
HOH
HOH
1123
A
HOH
1124
6
HOH
HOH
1124
A
HOH
1125
6
HOH
HOH
1125
A
HOH
1126
6
HOH
HOH
1126
A
HOH
1127
6
HOH
HOH
1127
A
HOH
1128
6
HOH
HOH
1128
A
HOH
1129
6
HOH
HOH
1129
A
HOH
1130
6
HOH
HOH
1130
A
HOH
1131
6
HOH
HOH
1131
A
HOH
1132
6
HOH
HOH
1132
A
HOH
1133
6
HOH
HOH
1133
A
HOH
1134
6
HOH
HOH
1134
A
HOH
1135
6
HOH
HOH
1135
A
HOH
1136
6
HOH
HOH
1136
A
HOH
1137
6
HOH
HOH
1137
A
HOH
1138
6
HOH
HOH
1138
A
HOH
1139
6
HOH
HOH
1139
A
HOH
1140
6
HOH
HOH
1140
A
HOH
1141
6
HOH
HOH
1141
A
HOH
1142
6
HOH
HOH
1142
A
HOH
1143
6
HOH
HOH
1143
A
HOH
1144
6
HOH
HOH
1144
A
HOH
1145
6
HOH
HOH
1145
A
HOH
1146
6
HOH
HOH
1146
A
HOH
1147
6
HOH
HOH
1147
A
HOH
1148
6
HOH
HOH
1148
A
HOH
1149
6
HOH
HOH
1149
A
HOH
1150
6
HOH
HOH
1150
A
HOH
1151
6
HOH
HOH
1151
A
HOH
1152
6
HOH
HOH
1152
A
HOH
1153
6
HOH
HOH
1153
A
HOH
1154
6
HOH
HOH
1154
A
HOH
1155
6
HOH
HOH
1155
A
HOH
1156
6
HOH
HOH
1156
A
HOH
1157
6
HOH
HOH
1157
A
HOH
1159
6
HOH
HOH
1159
A
HOH
1160
6
HOH
HOH
1160
A
HOH
1161
6
HOH
HOH
1161
A
HOH
1162
6
HOH
HOH
1162
A
HOH
1163
6
HOH
HOH
1163
A
HOH
1164
6
HOH
HOH
1164
A
HOH
1165
6
HOH
HOH
1165
A
HOH
1166
6
HOH
HOH
1166
A
HOH
1167
6
HOH
HOH
1167
A
HOH
1168
6
HOH
HOH
1168
A
HOH
1169
6
HOH
HOH
1169
A
HOH
1170
6
HOH
HOH
1170
A
HOH
1171
6
HOH
HOH
1171
A
HOH
1172
6
HOH
HOH
1172
A
HOH
1173
6
HOH
HOH
1173
A
HOH
1174
6
HOH
HOH
1174
A
HOH
1175
6
HOH
HOH
1175
A
HOH
1176
6
HOH
HOH
1176
A
HOH
1177
6
HOH
HOH
1177
A
HOH
1178
6
HOH
HOH
1178
A
HOH
1179
6
HOH
HOH
1179
A
HOH
1180
6
HOH
HOH
1180
A
HOH
1181
6
HOH
HOH
1181
A
HOH
1182
6
HOH
HOH
1182
A
HOH
1183
6
HOH
HOH
1183
A
HOH
1184
6
HOH
HOH
1184
A
HOH
1185
6
HOH
HOH
1185
A
HOH
1186
6
HOH
HOH
1186
A
HOH
1187
6
HOH
HOH
1187
A
HOH
1188
6
HOH
HOH
1188
A
HOH
1189
6
HOH
HOH
1189
A
HOH
1190
6
HOH
HOH
1190
A
HOH
1191
6
HOH
HOH
1191
A
HOH
1192
6
HOH
HOH
1192
A
HOH
1193
6
HOH
HOH
1193
A
HOH
1194
6
HOH
HOH
1194
A
HOH
1195
6
HOH
HOH
1195
A
HOH
1196
6
HOH
HOH
1196
A
HOH
1197
6
HOH
HOH
1197
A
HOH
1198
6
HOH
HOH
1198
A
HOH
1199
6
HOH
HOH
1199
A
HOH
1200
6
HOH
HOH
1200
A
HOH
1201
6
HOH
HOH
1201
A
HOH
1202
6
HOH
HOH
1202
A
HOH
1203
6
HOH
HOH
1203
A
HOH
1204
6
HOH
HOH
1204
A
HOH
1205
6
HOH
HOH
1205
A
HOH
1206
6
HOH
HOH
1206
A
HOH
1207
6
HOH
HOH
1207
A
HOH
1208
6
HOH
HOH
1208
A
HOH
1209
6
HOH
HOH
1209
A
HOH
1210
6
HOH
HOH
1210
A
VAL
5
n
1
VAL
5
A
THR
6
n
2
THR
6
A
SER
7
n
3
SER
7
A
ILE
8
n
4
ILE
8
A
LYS
9
n
5
LYS
9
A
LEU
10
n
6
LEU
10
A
VAL
11
n
7
VAL
11
A
LEU
12
n
8
LEU
12
A
LEU
13
n
9
LEU
13
A
GLY
14
n
10
GLY
14
A
GLU
15
n
11
GLU
15
A
ALA
16
n
12
ALA
16
A
ALA
17
n
13
ALA
17
A
VAL
18
n
14
VAL
18
A
GLY
19
n
15
GLY
19
A
LYS
20
n
16
LYS
20
A
SER
21
n
17
SER
21
A
SER
22
n
18
SER
22
A
ILE
23
n
19
ILE
23
A
VAL
24
n
20
VAL
24
A
LEU
25
n
21
LEU
25
A
ARG
26
n
22
ARG
26
A
PHE
27
n
23
PHE
27
A
VAL
28
n
24
VAL
28
A
SER
29
n
25
SER
29
A
ASN
30
n
26
ASN
30
A
ASP
31
n
27
ASP
31
A
PHE
32
n
28
PHE
32
A
ALA
33
n
29
ALA
33
A
GLU
34
n
30
GLU
34
A
ASN
35
n
31
ASN
35
A
LYS
36
n
32
LYS
36
A
GLU
37
n
33
GLU
37
A
PRO
38
n
34
PRO
38
A
THR
39
n
35
THR
39
A
ILE
40
n
36
ILE
40
A
GLY
41
n
37
GLY
41
A
ALA
42
n
38
ALA
42
A
ALA
43
n
39
ALA
43
A
PHE
44
n
40
PHE
44
A
LEU
45
n
41
LEU
45
A
THR
46
n
42
THR
46
A
GLN
47
n
43
GLN
47
A
ARG
48
n
44
ARG
48
A
VAL
49
n
45
VAL
49
A
THR
50
n
46
THR
50
A
ILE
51
n
47
ILE
51
A
ASN
52
n
48
ASN
52
A
GLU
53
n
49
GLU
53
A
HIS
54
n
50
HIS
54
A
THR
55
n
51
THR
55
A
VAL
56
n
52
VAL
56
A
LYS
57
n
53
LYS
57
A
PHE
58
n
54
PHE
58
A
GLU
59
n
55
GLU
59
A
ILE
60
n
56
ILE
60
A
TRP
61
n
57
TRP
61
A
ASP
62
n
58
ASP
62
A
THR
63
n
59
THR
63
A
ALA
64
n
60
ALA
64
A
GLY
65
n
61
GLY
65
A
GLN
66
n
62
GLN
66
A
GLU
67
n
63
GLU
67
A
ARG
68
n
64
ARG
68
A
PHE
69
n
65
PHE
69
A
ALA
70
n
66
ALA
70
A
SER
71
n
67
SER
71
A
LEU
72
n
68
LEU
72
A
ALA
73
n
69
ALA
73
A
PRO
74
n
70
PRO
74
A
MHO
75
n
71
MHO
75
A
TYR
76
n
72
TYR
76
A
TYR
77
n
73
TYR
77
A
ARG
78
n
74
ARG
78
A
ASN
79
n
75
ASN
79
A
ALA
80
n
76
ALA
80
A
GLN
81
n
77
GLN
81
A
ALA
82
n
78
ALA
82
A
ALA
83
n
79
ALA
83
A
LEU
84
n
80
LEU
84
A
VAL
85
n
81
VAL
85
A
VAL
86
n
82
VAL
86
A
TYR
87
n
83
TYR
87
A
ASP
88
n
84
ASP
88
A
VAL
89
n
85
VAL
89
A
THR
90
n
86
THR
90
A
LYS
91
n
87
LYS
91
A
PRO
92
n
88
PRO
92
A
GLN
93
n
89
GLN
93
A
SER
94
n
90
SER
94
A
PHE
95
n
91
PHE
95
A
ILE
96
n
92
ILE
96
A
LYS
97
n
93
LYS
97
A
ALA
98
n
94
ALA
98
A
ARG
99
n
95
ARG
99
A
HIS
100
n
96
HIS
100
A
TRP
101
n
97
TRP
101
A
VAL
102
n
98
VAL
102
A
LYS
103
n
99
LYS
103
A
GLU
104
n
100
GLU
104
A
LEU
105
n
101
LEU
105
A
HIS
106
n
102
HIS
106
A
GLU
107
n
103
GLU
107
A
GLN
108
n
104
GLN
108
A
ALA
109
n
105
ALA
109
A
SER
110
n
106
SER
110
A
LYS
111
n
107
LYS
111
A
ASP
112
n
108
ASP
112
A
ILE
113
n
109
ILE
113
A
ILE
114
n
110
ILE
114
A
ILE
115
n
111
ILE
115
A
ALA
116
n
112
ALA
116
A
LEU
117
n
113
LEU
117
A
VAL
118
n
114
VAL
118
A
GLY
119
n
115
GLY
119
A
ASN
120
n
116
ASN
120
A
LYS
121
n
117
LYS
121
A
ILE
122
n
118
ILE
122
A
ASP
123
n
119
ASP
123
A
MHO
124
n
120
MHO
124
A
LEU
125
n
121
LEU
125
A
GLN
126
n
122
GLN
126
A
GLU
127
n
123
GLU
127
A
GLY
128
n
124
GLY
128
A
GLY
129
n
125
GLY
129
A
GLU
130
n
126
GLU
130
A
ARG
131
n
127
ARG
131
A
LYS
132
n
128
LYS
132
A
VAL
133
n
129
VAL
133
A
ALA
134
n
130
ALA
134
A
ARG
135
n
131
ARG
135
A
GLU
136
n
132
GLU
136
A
GLU
137
n
133
GLU
137
A
GLY
138
n
134
GLY
138
A
GLU
139
n
135
GLU
139
A
LYS
140
n
136
LYS
140
A
LEU
141
n
137
LEU
141
A
ALA
142
n
138
ALA
142
A
GLU
143
n
139
GLU
143
A
GLU
144
n
140
GLU
144
A
LYS
145
n
141
LYS
145
A
GLY
146
n
142
GLY
146
A
LEU
147
n
143
LEU
147
A
LEU
148
n
144
LEU
148
A
PHE
149
n
145
PHE
149
A
PHE
150
n
146
PHE
150
A
GLU
151
n
147
GLU
151
A
THR
152
n
148
THR
152
A
SER
153
n
149
SER
153
A
ALA
154
n
150
ALA
154
A
LYS
155
n
151
LYS
155
A
THR
156
n
152
THR
156
A
GLY
157
n
153
GLY
157
A
GLU
158
n
154
GLU
158
A
ASN
159
n
155
ASN
159
A
VAL
160
n
156
VAL
160
A
ASN
161
n
157
ASN
161
A
ASP
162
n
158
ASP
162
A
VAL
163
n
159
VAL
163
A
PHE
164
n
160
PHE
164
A
LEU
165
n
161
LEU
165
A
GLY
166
n
162
GLY
166
A
ILE
167
n
163
ILE
167
A
GLY
168
n
164
GLY
168
A
GLU
169
n
165
GLU
169
A
LYS
170
n
166
LYS
170
A
ILE
171
n
167
ILE
171
A
PRO
172
n
168
PRO
172
A
LEU
173
n
169
LEU
173
A
LYS
174
n
170
LYS
174
A
0.1720000
0.1790000
0.1710000
0.1780000
0.2210000
0.2280000
152
166
5.
5.
2865
author_defined_assembly
1
monomeric
A
SER
21
A
OG
SER
17
1_555
A
MG
601
B
MG
MG
1_555
A
THR
39
A
OG1
THR
35
1_555
83.6
A
SER
21
A
OG
SER
17
1_555
A
MG
601
B
MG
MG
1_555
A
GNP
501
D
O2B
GNP
1_555
92.4
A
THR
39
A
OG1
THR
35
1_555
A
MG
601
B
MG
MG
1_555
A
GNP
501
D
O2B
GNP
1_555
175.1
A
SER
21
A
OG
SER
17
1_555
A
MG
601
B
MG
MG
1_555
A
GNP
501
D
O1G
GNP
1_555
171.8
A
THR
39
A
OG1
THR
35
1_555
A
MG
601
B
MG
MG
1_555
A
GNP
501
D
O1G
GNP
1_555
88.2
A
GNP
501
D
O2B
GNP
1_555
A
MG
601
B
MG
MG
1_555
A
GNP
501
D
O1G
GNP
1_555
95.9
A
SER
21
A
OG
SER
17
1_555
A
MG
601
B
MG
MG
1_555
A
HOH
1001
F
O
HOH
1_555
89.3
A
THR
39
A
OG1
THR
35
1_555
A
MG
601
B
MG
MG
1_555
A
HOH
1001
F
O
HOH
1_555
87.8
A
GNP
501
D
O2B
GNP
1_555
A
MG
601
B
MG
MG
1_555
A
HOH
1001
F
O
HOH
1_555
89.3
A
GNP
501
D
O1G
GNP
1_555
A
MG
601
B
MG
MG
1_555
A
HOH
1001
F
O
HOH
1_555
90.5
A
SER
21
A
OG
SER
17
1_555
A
MG
601
B
MG
MG
1_555
A
HOH
1002
F
O
HOH
1_555
87.9
A
THR
39
A
OG1
THR
35
1_555
A
MG
601
B
MG
MG
1_555
A
HOH
1002
F
O
HOH
1_555
91.7
A
GNP
501
D
O2B
GNP
1_555
A
MG
601
B
MG
MG
1_555
A
HOH
1002
F
O
HOH
1_555
91.0
A
GNP
501
D
O1G
GNP
1_555
A
MG
601
B
MG
MG
1_555
A
HOH
1002
F
O
HOH
1_555
92.1
A
HOH
1001
F
O
HOH
1_555
A
MG
601
B
MG
MG
1_555
A
HOH
1002
F
O
HOH
1_555
177.3
A
HIS
54
A
NE2
HIS
50
1_555
A
NI
602
C
NI
NI
1_555
A
GDP
502
E
N7
GDP
1_555
91.1
A
HIS
54
A
NE2
HIS
50
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1016
F
O
HOH
1_555
87.5
A
GDP
502
E
N7
GDP
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1016
F
O
HOH
1_555
93.8
A
HIS
54
A
NE2
HIS
50
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1154
F
O
HOH
1_555
94.6
A
GDP
502
E
N7
GDP
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1154
F
O
HOH
1_555
89.6
A
HOH
1016
F
O
HOH
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1154
F
O
HOH
1_555
175.9
A
HIS
54
A
NE2
HIS
50
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1155
F
O
HOH
1_555
89.1
A
GDP
502
E
N7
GDP
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1155
F
O
HOH
1_555
171.5
A
HOH
1016
F
O
HOH
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1155
F
O
HOH
1_555
94.7
A
HOH
1154
F
O
HOH
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1155
F
O
HOH
1_555
81.9
A
HIS
54
A
NE2
HIS
50
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1156
F
O
HOH
1_555
178.2
A
GDP
502
E
N7
GDP
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1156
F
O
HOH
1_555
89.4
A
HOH
1016
F
O
HOH
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1156
F
O
HOH
1_555
94.2
A
HOH
1154
F
O
HOH
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1156
F
O
HOH
1_555
83.7
A
HOH
1155
F
O
HOH
1_555
A
NI
602
C
NI
NI
1_555
A
HOH
1156
F
O
HOH
1_555
90.2
A
MHO
75
S-OXYMETHIONINE
A
MHO
71
MET
A
MHO
124
S-OXYMETHIONINE
A
MHO
120
MET
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
ILE
51
A
O
ILE
47
A
N
HIS
54
A
N
HIS
50
A
N
LYS
57
A
N
LYS
53
A
O
THR
6
A
O
THR
2
A
N
VAL
11
A
N
VAL
7
A
O
ALA
82
A
O
ALA
78
A
N
ALA
83
A
N
ALA
79
A
O
ILE
114
A
O
ILE
110
A
N
LEU
117
A
N
LEU
113
A
O
LEU
148
A
O
LEU
144
1
12.78
1.90
113.40
126.18
A
A
A
CA
CB
CG
TYR
TYR
TYR
77
77
77
N
1
3.88
0.50
120.30
124.18
A
A
A
NE
CZ
NH1
ARG
ARG
ARG
78
78
78
N
1
3.97
0.50
120.30
124.27
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
99
99
99
N
1
A
ASN
52
55.51
-117.36
1
A
GLU
127
-132.13
-130.65
0.2280000
0.1780000
0.1790000
0.1780000
1.48
31.00
660
1673
33452
33452
610
5.0
94.2
RANDOM
1
FREE R
0.0
0.0
MOLECULAR REPLACEMENT
5P21
ENGH AND HUBER
1
0.
1609.
1.48
31.00
209
1662
62
0
1391
0.01
0.04
0.00
0.027
0.04
0.06
0.01
0.00
0.06
0.00
34
1.48
20.0
1EK0
146199
33345
0.0
0.0
0.0260000
1
27.55
4.4
93.9
0.2140000
1.47
1.55
5.22
5853
3.2
90.0
phasing
AMoRE
refinement
SHELXL-97
data collection
MAR345
data scaling
XDS
GPPNHP-BOUND YPT51 AT 1.48 A RESOLUTION
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
6
N
N
A
GLY
19
A
GLY
15
HELX_P
A
ASN
30
A
ASN
26
1
1
12
A
GLN
66
A
GLN
62
HELX_P
A
ALA
73
A
ALA
69
5
2
8
A
LYS
91
A
LYS
87
HELX_P
A
ALA
109
A
ALA
105
1
3
19
A
ALA
134
A
ALA
130
HELX_P
A
GLY
146
A
GLY
142
1
4
13
A
ASN
159
A
ASN
155
HELX_P
A
GLU
169
A
GLU
165
1
5
11
covale
1.331
both
A
PRO
74
A
C
PRO
70
1_555
A
MHO
75
A
N
MHO
71
1_555
covale
1.330
both
A
MHO
75
A
C
MHO
71
1_555
A
TYR
76
A
N
TYR
72
1_555
covale
1.335
both
A
ASP
123
A
C
ASP
119
1_555
A
MHO
124
A
N
MHO
120
1_555
covale
1.322
both
A
MHO
124
A
C
MHO
120
1_555
A
LEU
125
A
N
LEU
121
1_555
metalc
2.061
A
SER
21
A
OG
SER
17
1_555
A
MG
601
B
MG
MG
1_555
metalc
2.220
A
THR
39
A
OG1
THR
35
1_555
A
MG
601
B
MG
MG
1_555
metalc
2.061
A
HIS
54
A
NE2
HIS
50
1_555
A
NI
602
C
NI
NI
1_555
metalc
2.024
A
GNP
501
D
O2B
GNP
1_555
A
MG
601
B
MG
MG
1_555
metalc
2.046
A
GNP
501
D
O1G
GNP
1_555
A
MG
601
B
MG
MG
1_555
metalc
2.032
A
GDP
502
E
N7
GDP
1_555
A
NI
602
C
NI
NI
1_555
metalc
2.155
A
MG
601
B
MG
MG
1_555
A
HOH
1001
F
O
HOH
1_555
metalc
2.062
A
MG
601
B
MG
MG
1_555
A
HOH
1002
F
O
HOH
1_555
metalc
2.064
A
NI
602
C
NI
NI
1_555
A
HOH
1016
F
O
HOH
1_555
metalc
2.143
A
NI
602
C
NI
NI
1_555
A
HOH
1154
F
O
HOH
1_555
metalc
2.142
A
NI
602
C
NI
NI
1_555
A
HOH
1155
F
O
HOH
1_555
metalc
2.125
A
NI
602
C
NI
NI
1_555
A
HOH
1156
F
O
HOH
1_555
ENDOCYTOSIS/EXOCYTOSIS
G PROTEIN, VESICULAR TRAFFIC, GTP HYDROLYSIS, YPT/RAB PROTEIN, ENDOCYTOSIS, HYDROLASE, ENDOCYTOSIS-EXOCYTOSIS COMPLEX
YPT51_YEAST
UNP
1
5
P36017
VTSIKLVLLGEAAVGKSSIVLRFVSNDFAENKEPTIGAAFLTQRVTINEHTVKFEIWDTAGQERFASLAPMYYRNAQAAL
VVYDVTKPQSFIKARHWVKELHEQASKDIIIALVGNKIDMLQEGGERKVAREEGEKLAEEKGLLFFETSAKTGENVNDVF
LGIGEKIPLK
5
174
1EK0
5
174
P36017
A
1
1
170
1
MET
modified residue
MHO
75
1EK0
A
P36017
UNP
75
71
1
MET
modified residue
MHO
124
1EK0
A
P36017
UNP
124
120
6
anti-parallel
parallel
parallel
parallel
parallel
A
ALA
42
A
ALA
38
A
ILE
51
A
ILE
47
A
HIS
54
A
HIS
50
A
THR
63
A
THR
59
A
THR
6
A
THR
2
A
LEU
13
A
LEU
9
A
ALA
82
A
ALA
78
A
ASP
88
A
ASP
84
A
ILE
114
A
ILE
110
A
ASN
120
A
ASN
116
A
LEU
148
A
LEU
144
A
GLU
151
A
GLU
147
BINDING SITE FOR RESIDUE MG A 601
A
MG
601
Software
5
BINDING SITE FOR RESIDUE NI A 602
A
NI
602
Software
6
BINDING SITE FOR RESIDUE GNP A 501
A
GNP
501
Software
29
BINDING SITE FOR RESIDUE GDP A 502
A
GDP
502
Software
22
A
SER
21
A
SER
17
5
1_555
A
THR
39
A
THR
35
5
1_555
A
GNP
501
D
GNP
5
1_555
A
HOH
1001
F
HOH
5
1_555
A
HOH
1002
F
HOH
5
1_555
A
HIS
54
A
HIS
50
6
1_555
A
GDP
502
E
GDP
6
1_555
A
HOH
1016
F
HOH
6
1_555
A
HOH
1154
F
HOH
6
1_555
A
HOH
1155
F
HOH
6
1_555
A
HOH
1156
F
HOH
6
1_555
A
ALA
16
A
ALA
12
29
1_555
A
ALA
17
A
ALA
13
29
1_555
A
VAL
18
A
VAL
14
29
1_555
A
GLY
19
A
GLY
15
29
1_555
A
LYS
20
A
LYS
16
29
1_555
A
SER
21
A
SER
17
29
1_555
A
SER
22
A
SER
18
29
1_555
A
PHE
32
A
PHE
28
29
1_555
A
ALA
33
A
ALA
29
29
1_555
A
GLU
34
A
GLU
30
29
1_555
A
PRO
38
A
PRO
34
29
1_555
A
THR
39
A
THR
35
29
1_555
A
GLY
65
A
GLY
61
29
1_555
A
ASN
120
A
ASN
116
29
1_555
A
LYS
121
A
LYS
117
29
1_555
A
ASP
123
A
ASP
119
29
1_555
A
MHO
124
A
MHO
120
29
1_555
A
SER
153
A
SER
149
29
1_555
A
ALA
154
A
ALA
150
29
1_555
A
LYS
155
A
LYS
151
29
1_555
A
MG
601
B
MG
29
1_555
A
HOH
1001
F
HOH
29
1_555
A
HOH
1002
F
HOH
29
1_555
A
HOH
1019
F
HOH
29
1_555
A
HOH
1044
F
HOH
29
1_555
A
HOH
1070
F
HOH
29
1_555
A
HOH
1091
F
HOH
29
1_555
A
HOH
1096
F
HOH
29
1_555
A
HOH
1112
F
HOH
29
1_555
A
PHE
44
A
PHE
40
22
6_555
A
THR
46
A
THR
42
22
6_555
A
ARG
48
A
ARG
44
22
6_555
A
ASN
52
A
ASN
48
22
1_555
A
HIS
54
A
HIS
50
22
1_555
A
LYS
57
A
LYS
53
22
6_555
A
GLU
130
A
GLU
126
22
2_655
A
ARG
131
A
ARG
127
22
2_655
A
LYS
132
A
LYS
128
22
2_655
A
GLU
169
A
GLU
165
22
1_555
A
LEU
173
A
LEU
169
22
1_555
A
NI
602
C
NI
22
1_555
A
HOH
1003
F
HOH
22
1_555
A
HOH
1013
F
HOH
22
1_555
A
HOH
1016
F
HOH
22
1_555
A
HOH
1023
F
HOH
22
1_555
A
HOH
1032
F
HOH
22
6_555
A
HOH
1039
F
HOH
22
6_555
A
HOH
1108
F
HOH
22
6_555
A
HOH
1140
F
HOH
22
2_655
A
HOH
1154
F
HOH
22
1_555
A
HOH
1156
F
HOH
22
1_555
169
P 61