0.011248
0.000000
0.003482
0.000000
0.028571
0.000000
0.000000
0.000000
0.017864
0.00000
0.00000
0.00000
Dumas, J.J.
Zhu, Z.
Connolly, J.L.
Lambright, D.G.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
107.20
90.00
88.900
35.000
58.600
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
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
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
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
P
N
138
N
O
N
139
N
O
N
140
N
O
N
141
N
N
N
142
R
P
N
143
N
O
N
144
N
O
N
145
N
O
N
146
S
P
N
147
N
O
N
148
N
O
N
149
N
O
N
150
N
C
N
151
R
C
N
152
N
O
N
153
S
C
N
154
N
O
N
155
R
C
N
156
N
O
N
157
R
C
Y
158
N
N
Y
159
N
C
Y
160
N
N
Y
161
N
C
Y
162
N
C
N
163
N
O
Y
164
N
N
Y
165
N
C
N
166
N
N
Y
167
N
N
Y
168
N
C
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
H
N
180
N
H
N
181
N
H
N
182
N
H
N
183
N
H
N
184
N
H
N
185
N
H
N
186
N
N
N
187
S
C
N
188
N
C
N
189
N
O
N
190
N
C
Y
191
N
C
Y
192
N
N
Y
193
N
C
Y
194
N
C
Y
195
N
N
N
196
N
O
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
O
N
208
N
H
N
209
N
H
N
210
N
N
N
211
S
C
N
212
N
C
N
213
N
O
N
214
S
C
N
215
N
C
N
216
N
C
N
217
N
C
N
218
N
O
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
H
N
230
N
H
N
231
N
H
N
232
N
N
N
233
S
C
N
234
N
C
N
235
N
O
N
236
N
C
N
237
N
C
N
238
N
C
N
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
H
N
253
N
H
N
254
N
N
N
255
S
C
N
256
N
C
N
257
N
O
N
258
N
C
N
259
N
C
N
260
N
C
N
261
N
C
N
262
N
N
N
263
N
O
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
N
N
280
S
C
N
281
N
C
N
282
N
O
N
283
N
C
N
284
N
C
N
285
N
S
N
286
N
C
N
287
N
O
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
MG
N
300
N
N
N
301
S
C
N
302
N
C
N
303
N
O
N
304
N
C
Y
305
N
C
Y
306
N
C
Y
307
N
C
Y
308
N
C
Y
309
N
C
Y
310
N
C
N
311
N
O
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
N
N
324
S
C
N
325
N
C
N
326
N
O
N
327
N
C
N
328
N
C
N
329
N
C
N
330
N
O
N
331
N
H
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
H
N
340
N
N
N
341
S
C
N
342
N
C
N
343
N
O
N
344
N
C
N
345
N
O
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
N
N
355
S
C
N
356
N
C
N
357
N
O
N
358
R
C
N
359
N
O
N
360
N
C
N
361
N
O
N
362
N
H
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
N
N
372
S
C
N
373
N
C
N
374
N
O
N
375
N
C
Y
376
N
C
Y
377
N
C
Y
378
N
C
Y
379
N
N
Y
380
N
C
Y
381
N
C
Y
382
N
C
Y
383
N
C
Y
384
N
C
N
385
N
O
N
386
N
H
N
387
N
H
N
388
N
H
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
N
N
399
S
C
N
400
N
C
N
401
N
O
N
402
N
C
Y
403
N
C
Y
404
N
C
Y
405
N
C
Y
406
N
C
Y
407
N
C
Y
408
N
C
N
409
N
O
N
410
N
O
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
N
N
423
S
C
N
424
N
C
N
425
N
O
N
426
N
C
N
427
N
C
N
428
N
C
N
429
N
O
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
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
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
doub
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
sing
N
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
Y
164
N
sing
Y
165
N
sing
Y
166
N
doub
N
167
N
sing
Y
168
N
sing
Y
169
N
sing
Y
170
N
doub
N
171
N
doub
Y
172
N
sing
Y
173
N
sing
N
174
N
sing
N
175
N
sing
Y
176
N
doub
N
177
N
sing
N
178
N
sing
Y
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
doub
N
187
N
sing
N
188
N
sing
N
189
N
sing
N
190
N
sing
Y
191
N
sing
Y
192
N
doub
Y
193
N
doub
N
194
N
sing
Y
195
N
sing
N
196
N
sing
Y
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
doub
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
doub
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
doub
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
doub
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
doub
N
295
N
sing
N
296
N
sing
N
297
N
sing
N
298
N
sing
Y
299
N
doub
Y
300
N
sing
Y
301
N
sing
N
302
N
sing
Y
303
N
doub
N
304
N
sing
Y
305
N
doub
N
306
N
sing
Y
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
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
doub
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
sing
N
345
N
sing
N
346
N
sing
N
347
N
doub
N
348
N
sing
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
doub
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
Y
368
N
doub
Y
369
N
sing
Y
370
N
sing
N
371
N
sing
Y
372
N
doub
Y
373
N
sing
Y
374
N
sing
N
375
N
sing
Y
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
doub
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
Y
396
N
doub
Y
397
N
sing
Y
398
N
sing
N
399
N
sing
Y
400
N
doub
N
401
N
sing
Y
402
N
doub
N
403
N
sing
Y
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
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
UK
Structure Fold.Des.
FODEFH
1263
0969-2126
7
413
423
10.1016/S0969-2126(99)80054-9
10196122
Structural basis of activation and GTP hydrolysis in Rab proteins.
1999
10.2210/pdb3rab/pdb
pdb_00003rab
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
IMAGE PLATE
1997-12
MARRESEARCH
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU RU200
19655.135
PROTEIN (RAB3A)
GTPASE DOMAIN
1
man
polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
522.196
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
1
syn
non-polymer
18.015
water
123
nat
water
no
no
NFDYMFKILIIGNSSVGKTSFLFRYADDSFTPAFVSTVGIDFKVKTIYRNDKRIKLQIWDTAGQERYRTITTAYYRGAMG
FILMYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDMEDERVVSSERGRQLADHLGFEFFEASAKDNINVKQTFE
RLVDVICEK
NFDYMFKILIIGNSSVGKTSFLFRYADDSFTPAFVSTVGIDFKVKTIYRNDKRIKLQIWDTAGQERYRTITTAYYRGAMG
FILMYDITNEESFNAVQDWSTQIKTYSWDNAQVLLVGNKCDMEDERVVSSERGRQLADHLGFEFFEASAKDNINVKQTFE
RLVDVICEK
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
Norway rat
Rattus
Escherichia
Escherichia coli
sample
10116
BRAIN
Rattus norvegicus
469008
Escherichia coli BL21(DE3)
BL21/DE3
PGEX
1
2.22
44.0
6.5
CRYSTALLIZATION CONDITIONS: 14%PEG-8000,50 MM NAMES, PH 6.5, 200 MM NACL
chem_comp_atom
chem_comp_bond
database_2
pdbx_initial_refinement_model
pdbx_struct_conn_angle
struct_conn
struct_site
repository
Initial release
Version format compliance
Version format compliance
Data collection
Database references
Derived calculations
Refinement description
1
0
1999-04-16
1
1
2008-04-26
1
2
2011-07-13
1
3
2023-09-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_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.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_site.pdbx_auth_asym_id
_struct_site.pdbx_auth_comp_id
_struct_site.pdbx_auth_seq_id
BNL
Y
RCSB
1998-11-16
REL
REL
MG
MAGNESIUM ION
GNP
PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER
HOH
water
5P21
PDB
experimental model
MG
201
2
MG
MG
201
A
GNP
200
3
GNP
GNP
200
A
HOH
300
4
HOH
HOH
300
A
HOH
301
4
HOH
HOH
301
A
HOH
302
4
HOH
HOH
302
A
HOH
303
4
HOH
HOH
303
A
HOH
304
4
HOH
HOH
304
A
HOH
305
4
HOH
HOH
305
A
HOH
306
4
HOH
HOH
306
A
HOH
307
4
HOH
HOH
307
A
HOH
308
4
HOH
HOH
308
A
HOH
309
4
HOH
HOH
309
A
HOH
310
4
HOH
HOH
310
A
HOH
312
4
HOH
HOH
312
A
HOH
313
4
HOH
HOH
313
A
HOH
314
4
HOH
HOH
314
A
HOH
315
4
HOH
HOH
315
A
HOH
316
4
HOH
HOH
316
A
HOH
317
4
HOH
HOH
317
A
HOH
318
4
HOH
HOH
318
A
HOH
319
4
HOH
HOH
319
A
HOH
320
4
HOH
HOH
320
A
HOH
321
4
HOH
HOH
321
A
HOH
322
4
HOH
HOH
322
A
HOH
323
4
HOH
HOH
323
A
HOH
324
4
HOH
HOH
324
A
HOH
326
4
HOH
HOH
326
A
HOH
327
4
HOH
HOH
327
A
HOH
328
4
HOH
HOH
328
A
HOH
329
4
HOH
HOH
329
A
HOH
331
4
HOH
HOH
331
A
HOH
332
4
HOH
HOH
332
A
HOH
333
4
HOH
HOH
333
A
HOH
334
4
HOH
HOH
334
A
HOH
335
4
HOH
HOH
335
A
HOH
337
4
HOH
HOH
337
A
HOH
338
4
HOH
HOH
338
A
HOH
339
4
HOH
HOH
339
A
HOH
342
4
HOH
HOH
342
A
HOH
343
4
HOH
HOH
343
A
HOH
344
4
HOH
HOH
344
A
HOH
345
4
HOH
HOH
345
A
HOH
346
4
HOH
HOH
346
A
HOH
348
4
HOH
HOH
348
A
HOH
349
4
HOH
HOH
349
A
HOH
350
4
HOH
HOH
350
A
HOH
351
4
HOH
HOH
351
A
HOH
353
4
HOH
HOH
353
A
HOH
355
4
HOH
HOH
355
A
HOH
359
4
HOH
HOH
359
A
HOH
360
4
HOH
HOH
360
A
HOH
362
4
HOH
HOH
362
A
HOH
364
4
HOH
HOH
364
A
HOH
367
4
HOH
HOH
367
A
HOH
369
4
HOH
HOH
369
A
HOH
370
4
HOH
HOH
370
A
HOH
371
4
HOH
HOH
371
A
HOH
373
4
HOH
HOH
373
A
HOH
374
4
HOH
HOH
374
A
HOH
375
4
HOH
HOH
375
A
HOH
377
4
HOH
HOH
377
A
HOH
378
4
HOH
HOH
378
A
HOH
380
4
HOH
HOH
380
A
HOH
383
4
HOH
HOH
383
A
HOH
384
4
HOH
HOH
384
A
HOH
386
4
HOH
HOH
386
A
HOH
387
4
HOH
HOH
387
A
HOH
390
4
HOH
HOH
390
A
HOH
395
4
HOH
HOH
395
A
HOH
398
4
HOH
HOH
398
A
HOH
399
4
HOH
HOH
399
A
HOH
403
4
HOH
HOH
403
A
HOH
406
4
HOH
HOH
406
A
HOH
502
4
HOH
HOH
502
A
HOH
504
4
HOH
HOH
504
A
HOH
505
4
HOH
HOH
505
A
HOH
506
4
HOH
HOH
506
A
HOH
507
4
HOH
HOH
507
A
HOH
509
4
HOH
HOH
509
A
HOH
510
4
HOH
HOH
510
A
HOH
512
4
HOH
HOH
512
A
HOH
513
4
HOH
HOH
513
A
HOH
515
4
HOH
HOH
515
A
HOH
517
4
HOH
HOH
517
A
HOH
518
4
HOH
HOH
518
A
HOH
519
4
HOH
HOH
519
A
HOH
521
4
HOH
HOH
521
A
HOH
523
4
HOH
HOH
523
A
HOH
524
4
HOH
HOH
524
A
HOH
525
4
HOH
HOH
525
A
HOH
526
4
HOH
HOH
526
A
HOH
528
4
HOH
HOH
528
A
HOH
529
4
HOH
HOH
529
A
HOH
531
4
HOH
HOH
531
A
HOH
535
4
HOH
HOH
535
A
HOH
537
4
HOH
HOH
537
A
HOH
538
4
HOH
HOH
538
A
HOH
541
4
HOH
HOH
541
A
HOH
542
4
HOH
HOH
542
A
HOH
543
4
HOH
HOH
543
A
HOH
547
4
HOH
HOH
547
A
HOH
548
4
HOH
HOH
548
A
HOH
549
4
HOH
HOH
549
A
HOH
551
4
HOH
HOH
551
A
HOH
554
4
HOH
HOH
554
A
HOH
556
4
HOH
HOH
556
A
HOH
558
4
HOH
HOH
558
A
HOH
559
4
HOH
HOH
559
A
HOH
560
4
HOH
HOH
560
A
HOH
561
4
HOH
HOH
561
A
HOH
564
4
HOH
HOH
564
A
HOH
565
4
HOH
HOH
565
A
HOH
566
4
HOH
HOH
566
A
HOH
568
4
HOH
HOH
568
A
HOH
571
4
HOH
HOH
571
A
HOH
572
4
HOH
HOH
572
A
HOH
576
4
HOH
HOH
576
A
HOH
577
4
HOH
HOH
577
A
HOH
579
4
HOH
HOH
579
A
HOH
580
4
HOH
HOH
580
A
HOH
582
4
HOH
HOH
582
A
HOH
584
4
HOH
HOH
584
A
HOH
586
4
HOH
HOH
586
A
HOH
587
4
HOH
HOH
587
A
HOH
588
4
HOH
HOH
588
A
ASN
18
n
1
ASN
18
A
PHE
19
n
2
PHE
19
A
ASP
20
n
3
ASP
20
A
TYR
21
n
4
TYR
21
A
MET
22
n
5
MET
22
A
PHE
23
n
6
PHE
23
A
LYS
24
n
7
LYS
24
A
ILE
25
n
8
ILE
25
A
LEU
26
n
9
LEU
26
A
ILE
27
n
10
ILE
27
A
ILE
28
n
11
ILE
28
A
GLY
29
n
12
GLY
29
A
ASN
30
n
13
ASN
30
A
SER
31
n
14
SER
31
A
SER
32
n
15
SER
32
A
VAL
33
n
16
VAL
33
A
GLY
34
n
17
GLY
34
A
LYS
35
n
18
LYS
35
A
THR
36
n
19
THR
36
A
SER
37
n
20
SER
37
A
PHE
38
n
21
PHE
38
A
LEU
39
n
22
LEU
39
A
PHE
40
n
23
PHE
40
A
ARG
41
n
24
ARG
41
A
TYR
42
n
25
TYR
42
A
ALA
43
n
26
ALA
43
A
ASP
44
n
27
ASP
44
A
ASP
45
n
28
ASP
45
A
SER
46
n
29
SER
46
A
PHE
47
n
30
PHE
47
A
THR
48
n
31
THR
48
A
PRO
49
n
32
PRO
49
A
ALA
50
n
33
ALA
50
A
PHE
51
n
34
PHE
51
A
VAL
52
n
35
VAL
52
A
SER
53
n
36
SER
53
A
THR
54
n
37
THR
54
A
VAL
55
n
38
VAL
55
A
GLY
56
n
39
GLY
56
A
ILE
57
n
40
ILE
57
A
ASP
58
n
41
ASP
58
A
PHE
59
n
42
PHE
59
A
LYS
60
n
43
LYS
60
A
VAL
61
n
44
VAL
61
A
LYS
62
n
45
LYS
62
A
THR
63
n
46
THR
63
A
ILE
64
n
47
ILE
64
A
TYR
65
n
48
TYR
65
A
ARG
66
n
49
ARG
66
A
ASN
67
n
50
ASN
67
A
ASP
68
n
51
ASP
68
A
LYS
69
n
52
LYS
69
A
ARG
70
n
53
ARG
70
A
ILE
71
n
54
ILE
71
A
LYS
72
n
55
LYS
72
A
LEU
73
n
56
LEU
73
A
GLN
74
n
57
GLN
74
A
ILE
75
n
58
ILE
75
A
TRP
76
n
59
TRP
76
A
ASP
77
n
60
ASP
77
A
THR
78
n
61
THR
78
A
ALA
79
n
62
ALA
79
A
GLY
80
n
63
GLY
80
A
GLN
81
n
64
GLN
81
A
GLU
82
n
65
GLU
82
A
ARG
83
n
66
ARG
83
A
TYR
84
n
67
TYR
84
A
ARG
85
n
68
ARG
85
A
THR
86
n
69
THR
86
A
ILE
87
n
70
ILE
87
A
THR
88
n
71
THR
88
A
THR
89
n
72
THR
89
A
ALA
90
n
73
ALA
90
A
TYR
91
n
74
TYR
91
A
TYR
92
n
75
TYR
92
A
ARG
93
n
76
ARG
93
A
GLY
94
n
77
GLY
94
A
ALA
95
n
78
ALA
95
A
MET
96
n
79
MET
96
A
GLY
97
n
80
GLY
97
A
PHE
98
n
81
PHE
98
A
ILE
99
n
82
ILE
99
A
LEU
100
n
83
LEU
100
A
MET
101
n
84
MET
101
A
TYR
102
n
85
TYR
102
A
ASP
103
n
86
ASP
103
A
ILE
104
n
87
ILE
104
A
THR
105
n
88
THR
105
A
ASN
106
n
89
ASN
106
A
GLU
107
n
90
GLU
107
A
GLU
108
n
91
GLU
108
A
SER
109
n
92
SER
109
A
PHE
110
n
93
PHE
110
A
ASN
111
n
94
ASN
111
A
ALA
112
n
95
ALA
112
A
VAL
113
n
96
VAL
113
A
GLN
114
n
97
GLN
114
A
ASP
115
n
98
ASP
115
A
TRP
116
n
99
TRP
116
A
SER
117
n
100
SER
117
A
THR
118
n
101
THR
118
A
GLN
119
n
102
GLN
119
A
ILE
120
n
103
ILE
120
A
LYS
121
n
104
LYS
121
A
THR
122
n
105
THR
122
A
TYR
123
n
106
TYR
123
A
SER
124
n
107
SER
124
A
TRP
125
n
108
TRP
125
A
ASP
126
n
109
ASP
126
A
ASN
127
n
110
ASN
127
A
ALA
128
n
111
ALA
128
A
GLN
129
n
112
GLN
129
A
VAL
130
n
113
VAL
130
A
LEU
131
n
114
LEU
131
A
LEU
132
n
115
LEU
132
A
VAL
133
n
116
VAL
133
A
GLY
134
n
117
GLY
134
A
ASN
135
n
118
ASN
135
A
LYS
136
n
119
LYS
136
A
CYS
137
n
120
CYS
137
A
ASP
138
n
121
ASP
138
A
MET
139
n
122
MET
139
A
GLU
140
n
123
GLU
140
A
ASP
141
n
124
ASP
141
A
GLU
142
n
125
GLU
142
A
ARG
143
n
126
ARG
143
A
VAL
144
n
127
VAL
144
A
VAL
145
n
128
VAL
145
A
SER
146
n
129
SER
146
A
SER
147
n
130
SER
147
A
GLU
148
n
131
GLU
148
A
ARG
149
n
132
ARG
149
A
GLY
150
n
133
GLY
150
A
ARG
151
n
134
ARG
151
A
GLN
152
n
135
GLN
152
A
LEU
153
n
136
LEU
153
A
ALA
154
n
137
ALA
154
A
ASP
155
n
138
ASP
155
A
HIS
156
n
139
HIS
156
A
LEU
157
n
140
LEU
157
A
GLY
158
n
141
GLY
158
A
PHE
159
n
142
PHE
159
A
GLU
160
n
143
GLU
160
A
PHE
161
n
144
PHE
161
A
PHE
162
n
145
PHE
162
A
GLU
163
n
146
GLU
163
A
ALA
164
n
147
ALA
164
A
SER
165
n
148
SER
165
A
ALA
166
n
149
ALA
166
A
LYS
167
n
150
LYS
167
A
ASP
168
n
151
ASP
168
A
ASN
169
n
152
ASN
169
A
ILE
170
n
153
ILE
170
A
ASN
171
n
154
ASN
171
A
VAL
172
n
155
VAL
172
A
LYS
173
n
156
LYS
173
A
GLN
174
n
157
GLN
174
A
THR
175
n
158
THR
175
A
PHE
176
n
159
PHE
176
A
GLU
177
n
160
GLU
177
A
ARG
178
n
161
ARG
178
A
LEU
179
n
162
LEU
179
A
VAL
180
n
163
VAL
180
A
ASP
181
n
164
ASP
181
A
VAL
182
n
165
VAL
182
A
ILE
183
n
166
ILE
183
A
CYS
184
n
167
CYS
184
A
GLU
185
n
168
GLU
185
A
LYS
186
n
169
LYS
186
A
author_defined_assembly
1
monomeric
A
THR
36
A
OG1
THR
19
1_555
A
MG
201
B
MG
MG
1_555
A
THR
54
A
OG1
THR
37
1_555
81.2
A
THR
36
A
OG1
THR
19
1_555
A
MG
201
B
MG
MG
1_555
A
GNP
200
C
O2G
GNP
1_555
166.8
A
THR
54
A
OG1
THR
37
1_555
A
MG
201
B
MG
MG
1_555
A
GNP
200
C
O2G
GNP
1_555
89.8
A
THR
36
A
OG1
THR
19
1_555
A
MG
201
B
MG
MG
1_555
A
GNP
200
C
O2B
GNP
1_555
91.0
A
THR
54
A
OG1
THR
37
1_555
A
MG
201
B
MG
MG
1_555
A
GNP
200
C
O2B
GNP
1_555
172.1
A
GNP
200
C
O2G
GNP
1_555
A
MG
201
B
MG
MG
1_555
A
GNP
200
C
O2B
GNP
1_555
98.1
A
THR
36
A
OG1
THR
19
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
301
D
O
HOH
1_555
95.3
A
THR
54
A
OG1
THR
37
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
301
D
O
HOH
1_555
94.3
A
GNP
200
C
O2G
GNP
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
301
D
O
HOH
1_555
94.9
A
GNP
200
C
O2B
GNP
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
301
D
O
HOH
1_555
85.3
A
THR
36
A
OG1
THR
19
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
318
D
O
HOH
1_555
87.6
A
THR
54
A
OG1
THR
37
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
318
D
O
HOH
1_555
91.9
A
GNP
200
C
O2G
GNP
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
318
D
O
HOH
1_555
83.1
A
GNP
200
C
O2B
GNP
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
318
D
O
HOH
1_555
88.8
A
HOH
301
D
O
HOH
1_555
A
MG
201
B
MG
MG
1_555
A
HOH
318
D
O
HOH
1_555
173.5
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
GLU
160
A
O
GLU
143
A
N
LEU
132
A
N
LEU
115
A
O
GLN
129
A
O
GLN
112
A
N
PHE
98
A
N
PHE
81
A
O
GLY
97
A
O
GLY
80
A
N
LEU
26
A
N
LEU
9
A
O
TYR
21
A
O
TYR
4
A
N
LYS
72
A
N
LYS
55
A
O
LYS
69
A
O
LYS
52
A
N
ARG
66
A
N
ARG
49
1
A
CG
ASN
18
A
CG
ASN
1
1
Y
1
A
OD1
ASN
18
A
OD1
ASN
1
1
Y
1
A
ND2
ASN
18
A
ND2
ASN
1
1
Y
1
A
CG
ASN
67
A
CG
ASN
50
1
Y
1
A
OD1
ASN
67
A
OD1
ASN
50
1
Y
1
A
ND2
ASN
67
A
ND2
ASN
50
1
Y
1
A
CG
GLU
82
A
CG
GLU
65
1
Y
1
A
CD
GLU
82
A
CD
GLU
65
1
Y
1
A
OE1
GLU
82
A
OE1
GLU
65
1
Y
1
A
OE2
GLU
82
A
OE2
GLU
65
1
Y
1
A
CG
ASP
126
A
CG
ASP
109
1
Y
1
A
OD1
ASP
126
A
OD1
ASP
109
1
Y
1
A
OD2
ASP
126
A
OD2
ASP
109
1
Y
1
A
CG
ASN
127
A
CG
ASN
110
1
Y
1
A
OD1
ASN
127
A
OD1
ASN
110
1
Y
1
A
ND2
ASN
127
A
ND2
ASN
110
1
Y
1
A
CG
LYS
173
A
CG
LYS
156
1
Y
1
A
CD
LYS
173
A
CD
LYS
156
1
Y
1
A
CE
LYS
173
A
CE
LYS
156
1
Y
1
A
NZ
LYS
173
A
NZ
LYS
156
1
Y
1
A
SG
CYS
184
A
SG
CYS
167
1
Y
13.0
0.2370000
0.1910000
2.0
8.0
10595
5.0
99.5
RANDOM
0.0
0.0
1
THROUGHOUT
2.0
MOLECULAR REPLACEMENT
5P21
2.0
8.0
123
1520
33
0
1364
0.007
1.3
24.2
1.2
0.2300000
0.1840000
99.5
2.0
20.0
3RAB
10595
-3.0
0.0630000
1
17.1
99.5
2.0
2.1
6.3
0.1970000
99.5
phasing
AMoRE
refinement
X-PLOR
3.1
data reduction
DENZO
data scaling
SCALEPACK
GPPNHP-BOUND RAB3A AT 2.0 A RESOLUTION
1
N
N
2
N
N
3
N
N
4
N
N
A
LYS
35
A
LYS
18
HELX_P
A
ASP
44
A
ASP
27
1
1
10
A
GLU
82
A
GLU
65
HELX_P
A
TYR
91
A
TYR
74
1
2
10
A
GLU
107
A
GLU
90
HELX_P
A
ASN
111
A
ASN
94
1
3
5
A
VAL
113
A
VAL
96
HELX_P
A
TYR
123
A
TYR
106
1
4
11
A
SER
147
A
SER
130
HELX_P
A
LEU
157
A
LEU
140
1
5
11
A
VAL
172
A
VAL
155
HELX_P
A
CYS
184
A
CYS
167
1
6
13
metalc
2.246
A
THR
36
A
OG1
THR
19
1_555
A
MG
201
B
MG
MG
1_555
metalc
2.272
A
THR
54
A
OG1
THR
37
1_555
A
MG
201
B
MG
MG
1_555
metalc
2.246
A
GNP
200
C
O2G
GNP
1_555
A
MG
201
B
MG
MG
1_555
metalc
2.258
A
GNP
200
C
O2B
GNP
1_555
A
MG
201
B
MG
MG
1_555
metalc
2.332
A
MG
201
B
MG
MG
1_555
A
HOH
301
D
O
HOH
1_555
metalc
2.403
A
MG
201
B
MG
MG
1_555
A
HOH
318
D
O
HOH
1_555
HYDROLASE
G PROTEIN, VESICULAR TRAFFICKING, GTP HYDROLYSIS, RAB PROTEIN, NEUROTRANSMITTER RELEASE, HYDROLASE
RAB3A_RAT
UNP
1
P63012
18
186
3RAB
18
186
P63012
A
1
1
169
6
parallel
parallel
parallel
parallel
anti-parallel
A
GLU
160
A
GLU
143
A
GLU
163
A
GLU
146
A
GLN
129
A
GLN
112
A
ASN
135
A
ASN
118
A
GLY
97
A
GLY
80
A
ASP
103
A
ASP
86
A
TYR
21
A
TYR
4
A
GLY
29
A
GLY
12
A
LYS
69
A
LYS
52
A
THR
78
A
THR
61
A
ILE
57
A
ILE
40
A
ARG
66
A
ARG
49
BINDING SITE FOR RESIDUE MG A 201
A
MG
201
Software
5
BINDING SITE FOR RESIDUE GNP A 200
A
GNP
200
Software
26
A
THR
36
A
THR
19
5
1_555
A
THR
54
A
THR
37
5
1_555
A
GNP
200
C
GNP
5
1_555
A
HOH
301
D
HOH
5
1_555
A
HOH
318
D
HOH
5
1_555
A
SER
31
A
SER
14
26
1_555
A
SER
32
A
SER
15
26
1_555
A
VAL
33
A
VAL
16
26
1_555
A
GLY
34
A
GLY
17
26
1_555
A
LYS
35
A
LYS
18
26
1_555
A
THR
36
A
THR
19
26
1_555
A
SER
37
A
SER
20
26
1_555
A
PHE
47
A
PHE
30
26
1_555
A
THR
48
A
THR
31
26
1_555
A
PRO
49
A
PRO
32
26
1_555
A
ALA
50
A
ALA
33
26
1_555
A
PHE
51
A
PHE
34
26
1_555
A
SER
53
A
SER
36
26
1_555
A
THR
54
A
THR
37
26
1_555
A
GLY
80
A
GLY
63
26
1_555
A
ASN
135
A
ASN
118
26
1_555
A
LYS
136
A
LYS
119
26
1_555
A
ASP
138
A
ASP
121
26
1_555
A
MET
139
A
MET
122
26
1_555
A
SER
165
A
SER
148
26
1_555
A
ALA
166
A
ALA
149
26
1_555
A
LYS
167
A
LYS
150
26
1_555
A
MG
201
B
MG
26
1_555
A
HOH
302
D
HOH
26
1_555
A
HOH
318
D
HOH
26
1_555
A
HOH
566
D
HOH
26
1_555
5
C 1 2 1