0.012570
0.007257
0.000000
0.000000
0.014515
0.000000
0.000000
0.000000
0.012811
0.00000
0.00000
0.00000
Oh, A.
Maurer, T.
Garrenton, L.S.
Pitts, K.
Anderson, D.J.
Skelton, N.J.
Fauber, B.P.
Pan, B.
Malek, S.
Stokoe, D.
Ludlam, M.
Bowman, K.K.
Wu, J.
Giannetti, A.M.
Starovasnik, M.A.
Mellman, I.
Jackson, P.K.
Ruldolph, J.
Fang, G.
Wang, W.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
9
90.00
90.00
120.00
79.553
79.553
78.055
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
C7 H6 N2
118.136
BENZIMIDAZOLE
non-polymer
C3 H7 N O2 S
121.158
y
CYSTEINE
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
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
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
Y
74
N
N
Y
75
N
C
Y
76
N
N
Y
77
N
C
Y
78
N
C
Y
79
N
C
Y
80
N
C
Y
81
N
C
Y
82
N
C
N
83
N
H
N
84
N
H
N
85
N
H
N
86
N
H
N
87
N
H
N
88
N
H
N
89
N
N
N
90
R
C
N
91
N
C
N
92
N
O
N
93
N
C
N
94
N
S
N
95
N
O
N
96
N
H
N
97
N
H
N
98
N
H
N
99
N
H
N
100
N
H
N
101
N
H
N
102
N
H
N
103
N
P
N
104
N
O
N
105
N
O
N
106
N
O
N
107
N
O
N
108
N
P
N
109
N
O
N
110
N
O
N
111
N
O
N
112
N
C
N
113
R
C
N
114
N
O
N
115
S
C
N
116
N
O
N
117
R
C
N
118
N
O
N
119
R
C
Y
120
N
N
Y
121
N
C
Y
122
N
N
Y
123
N
C
N
124
N
C
N
125
N
O
N
126
N
N
N
127
N
C
N
128
N
N
N
129
N
N
Y
130
N
C
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
H
N
138
N
H
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
N
N
147
S
C
N
148
N
C
N
149
N
O
N
150
N
C
N
151
N
C
N
152
N
C
N
153
N
O
N
154
N
N
N
155
N
O
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
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
N
N
167
S
C
N
168
N
C
N
169
N
O
N
170
N
C
N
171
N
C
N
172
N
C
N
173
N
O
N
174
N
O
N
175
N
O
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
N
N
186
N
C
N
187
N
C
N
188
N
O
N
189
N
O
N
190
N
H
N
191
N
H
N
192
N
H
N
193
N
H
N
194
N
H
N
195
N
N
N
196
S
C
N
197
N
C
N
198
N
O
N
199
N
C
Y
200
N
C
Y
201
N
N
Y
202
N
C
Y
203
N
C
Y
204
N
N
N
205
N
O
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
H
N
216
N
O
N
217
N
H
N
218
N
H
N
219
N
N
N
220
S
C
N
221
N
C
N
222
N
O
N
223
S
C
N
224
N
C
N
225
N
C
N
226
N
C
N
227
N
O
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
H
N
237
N
H
N
238
N
H
N
239
N
H
N
240
N
H
N
241
N
N
N
242
S
C
N
243
N
C
N
244
N
O
N
245
N
C
N
246
N
C
N
247
N
C
N
248
N
C
N
249
N
O
N
250
N
H
N
251
N
H
N
252
N
H
N
253
N
H
N
254
N
H
N
255
N
H
N
256
N
H
N
257
N
H
N
258
N
H
N
259
N
H
N
260
N
H
N
261
N
H
N
262
N
H
N
263
N
N
N
264
S
C
N
265
N
C
N
266
N
O
N
267
N
C
N
268
N
C
N
269
N
C
N
270
N
C
N
271
N
N
N
272
N
O
N
273
N
H
N
274
N
H
N
275
N
H
N
276
N
H
N
277
N
H
N
278
N
H
N
279
N
H
N
280
N
H
N
281
N
H
N
282
N
H
N
283
N
H
N
284
N
H
N
285
N
H
N
286
N
H
N
287
N
H
N
288
N
N
N
289
S
C
N
290
N
C
N
291
N
O
N
292
N
C
N
293
N
C
N
294
N
S
N
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
MG
N
309
N
N
N
310
S
C
N
311
N
C
N
312
N
O
N
313
N
C
Y
314
N
C
Y
315
N
C
Y
316
N
C
Y
317
N
C
Y
318
N
C
Y
319
N
C
N
320
N
O
N
321
N
H
N
322
N
H
N
323
N
H
N
324
N
H
N
325
N
H
N
326
N
H
N
327
N
H
N
328
N
H
N
329
N
H
N
330
N
H
N
331
N
H
N
332
N
N
N
333
S
C
N
334
N
C
N
335
N
O
N
336
N
C
N
337
N
C
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
N
354
N
O
N
355
N
O
N
356
N
H
N
357
N
H
N
358
N
H
N
359
N
H
N
360
N
H
N
361
N
H
N
362
N
H
N
363
N
N
N
364
S
C
N
365
N
C
N
366
N
O
N
367
R
C
N
368
N
O
N
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
N
N
381
S
C
N
382
N
C
N
383
N
O
N
384
N
C
Y
385
N
C
Y
386
N
C
Y
387
N
C
Y
388
N
C
Y
389
N
C
Y
390
N
C
N
391
N
O
N
392
N
O
N
393
N
H
N
394
N
H
N
395
N
H
N
396
N
H
N
397
N
H
N
398
N
H
N
399
N
H
N
400
N
H
N
401
N
H
N
402
N
H
N
403
N
H
N
404
N
N
N
405
S
C
N
406
N
C
N
407
N
O
N
408
N
C
N
409
N
C
N
410
N
C
N
411
N
O
N
412
N
H
N
413
N
H
N
414
N
H
N
415
N
H
N
416
N
H
N
417
N
H
N
418
N
H
N
419
N
H
N
420
N
H
N
421
N
H
N
422
N
H
N
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
Y
70
N
sing
Y
71
N
sing
N
72
N
sing
Y
73
N
doub
N
74
N
sing
Y
75
N
sing
Y
76
N
doub
Y
77
N
sing
Y
78
N
sing
N
79
N
sing
Y
80
N
doub
N
81
N
sing
Y
82
N
sing
N
83
N
sing
Y
84
N
doub
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
doub
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
sing
N
98
N
sing
N
99
N
doub
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
doub
N
107
N
sing
N
108
N
sing
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
sing
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
sing
N
127
N
sing
Y
128
N
sing
Y
129
N
sing
Y
130
N
doub
N
131
N
sing
Y
132
N
sing
N
133
N
sing
Y
134
N
doub
N
135
N
doub
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
sing
N
149
N
sing
N
150
N
doub
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
doub
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
doub
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
doub
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
doub
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
Y
201
N
sing
Y
202
N
doub
Y
203
N
doub
N
204
N
sing
Y
205
N
sing
N
206
N
sing
Y
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
doub
N
220
N
sing
N
221
N
sing
N
222
N
sing
N
223
N
sing
N
224
N
sing
N
225
N
sing
N
226
N
sing
N
227
N
sing
N
228
N
sing
N
229
N
sing
N
230
N
sing
N
231
N
sing
N
232
N
sing
N
233
N
sing
N
234
N
sing
N
235
N
sing
N
236
N
sing
N
237
N
sing
N
238
N
sing
N
239
N
sing
N
240
N
doub
N
241
N
sing
N
242
N
sing
N
243
N
sing
N
244
N
sing
N
245
N
sing
N
246
N
sing
N
247
N
sing
N
248
N
sing
N
249
N
sing
N
250
N
sing
N
251
N
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
sing
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
N
261
N
doub
N
262
N
sing
N
263
N
sing
N
264
N
sing
N
265
N
sing
N
266
N
sing
N
267
N
sing
N
268
N
sing
N
269
N
sing
N
270
N
sing
N
271
N
sing
N
272
N
sing
N
273
N
sing
N
274
N
sing
N
275
N
sing
N
276
N
sing
N
277
N
sing
N
278
N
sing
N
279
N
sing
N
280
N
sing
N
281
N
sing
N
282
N
sing
N
283
N
sing
N
284
N
sing
N
285
N
doub
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
doub
N
305
N
sing
N
306
N
sing
N
307
N
sing
N
308
N
sing
Y
309
N
doub
Y
310
N
sing
Y
311
N
sing
N
312
N
sing
Y
313
N
doub
N
314
N
sing
Y
315
N
doub
N
316
N
sing
Y
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
doub
N
328
N
sing
N
329
N
sing
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
N
334
N
sing
N
335
N
sing
N
336
N
sing
N
337
N
sing
N
338
N
sing
N
339
N
sing
N
340
N
sing
N
341
N
sing
N
342
N
sing
N
343
N
sing
N
344
N
doub
N
345
N
sing
N
346
N
sing
N
347
N
sing
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
doub
N
358
N
sing
N
359
N
sing
N
360
N
sing
N
361
N
sing
N
362
N
sing
N
363
N
sing
N
364
N
sing
N
365
N
sing
N
366
N
sing
N
367
N
sing
N
368
N
sing
N
369
N
sing
N
370
N
sing
N
371
N
sing
N
372
N
sing
N
373
N
doub
N
374
N
sing
N
375
N
sing
N
376
N
sing
N
377
N
sing
Y
378
N
doub
Y
379
N
sing
Y
380
N
sing
N
381
N
sing
Y
382
N
doub
N
383
N
sing
Y
384
N
doub
N
385
N
sing
Y
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
N
393
N
sing
N
394
N
sing
N
395
N
sing
N
396
N
sing
N
397
N
doub
N
398
N
sing
N
399
N
sing
N
400
N
sing
N
401
N
sing
N
402
N
sing
N
403
N
sing
N
404
N
sing
N
405
N
sing
N
406
N
sing
N
407
N
sing
N
408
N
sing
US
Proc.Natl.Acad.Sci.USA
PNASA6
0040
0027-8424
109
5299
5304
10.1073/pnas.1116510109
22431598
Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity.
2012
10.2210/pdb4dsu/pdb
pdb_00004dsu
1.000000
0.000000
0.000000
0.000000
1.000000
0.000000
0.000000
0.000000
1.000000
0.00000
0.00000
0.00000
93
1
CCD
2010-09-03
ADSC QUANTUM 315
Liquid Nitrogen cooled Dual Crystal
SINGLE WAVELENGTH
M
x-ray
1
1.00000
1.0
5.0.2
ALS
1.00000
SYNCHROTRON
ALS BEAMLINE 5.0.2
21530.574
GTPase KRas, isoform 2B
3.6.-.-
G12D
1
man
polymer
443.201
GUANOSINE-5'-DIPHOSPHATE
1
syn
non-polymer
24.305
MAGNESIUM ION
1
syn
non-polymer
118.136
BENZIMIDAZOLE
1
syn
non-polymer
18.015
water
63
nat
water
KRas 4B, K-Ras 2, Ki-Ras, c-K-ras, c-Ki-ras, GTPase KRas, N-terminally processed
no
no
GSTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFL
CVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTL
VREIRKHKEKMSKDGKKKKKKSKTKCVIM
GSTEYKLVVVGADGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFL
CVFAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTL
VREIRKHKEKMSKDGKKKKKKSKTKCVIM
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
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
n
human
sample
KRAS, KRAS2, RASK2
9606
Homo sapiens
562
Escherichia coli
2.21
44.29
VAPOR DIFFUSION, SITTING DROP
8.5
0.2 uL + 0.2 uL drops containing 40 mg/mL KRas, 0.1 M TrisCl, 25% polyethylene glycol 4000, 0.2 M NaOAc, 2% benzamidine-HCl, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K
277
chem_comp_atom
chem_comp_bond
database_2
pdbx_struct_conn_angle
struct_conn
struct_ref_seq_dif
struct_site
repository
Initial release
Database references
Database references
Data collection
Database references
Derived calculations
1
0
2012-04-04
1
1
2012-04-18
1
2
2012-06-06
1
3
2024-02-28
_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_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
2012-02-19
REL
REL
GDP
GUANOSINE-5'-DIPHOSPHATE
MG
MAGNESIUM ION
BZI
BENZIMIDAZOLE
HOH
water
THE SEQUENCE MATCHES UNIPROT ENTRY P01116, ISOFORM 2B WITH IDENTIFIER P01116-2.
GDP
1
2
GDP
GDP
201
A
MG
1
3
MG
MG
202
A
BZI
1
4
BZI
BZI
203
A
HOH
1
5
HOH
HOH
301
A
HOH
2
5
HOH
HOH
302
A
HOH
3
5
HOH
HOH
303
A
HOH
4
5
HOH
HOH
304
A
HOH
5
5
HOH
HOH
305
A
HOH
6
5
HOH
HOH
306
A
HOH
7
5
HOH
HOH
307
A
HOH
8
5
HOH
HOH
308
A
HOH
9
5
HOH
HOH
309
A
HOH
10
5
HOH
HOH
310
A
HOH
11
5
HOH
HOH
311
A
HOH
12
5
HOH
HOH
312
A
HOH
13
5
HOH
HOH
313
A
HOH
14
5
HOH
HOH
314
A
HOH
15
5
HOH
HOH
315
A
HOH
16
5
HOH
HOH
316
A
HOH
18
5
HOH
HOH
317
A
HOH
19
5
HOH
HOH
318
A
HOH
20
5
HOH
HOH
319
A
HOH
21
5
HOH
HOH
320
A
HOH
22
5
HOH
HOH
321
A
HOH
24
5
HOH
HOH
322
A
HOH
25
5
HOH
HOH
323
A
HOH
26
5
HOH
HOH
324
A
HOH
28
5
HOH
HOH
325
A
HOH
29
5
HOH
HOH
326
A
HOH
30
5
HOH
HOH
327
A
HOH
31
5
HOH
HOH
328
A
HOH
32
5
HOH
HOH
329
A
HOH
33
5
HOH
HOH
330
A
HOH
34
5
HOH
HOH
331
A
HOH
35
5
HOH
HOH
332
A
HOH
36
5
HOH
HOH
333
A
HOH
37
5
HOH
HOH
334
A
HOH
38
5
HOH
HOH
335
A
HOH
39
5
HOH
HOH
336
A
HOH
40
5
HOH
HOH
337
A
HOH
41
5
HOH
HOH
338
A
HOH
42
5
HOH
HOH
339
A
HOH
43
5
HOH
HOH
340
A
HOH
44
5
HOH
HOH
341
A
HOH
45
5
HOH
HOH
342
A
HOH
46
5
HOH
HOH
343
A
HOH
47
5
HOH
HOH
344
A
HOH
48
5
HOH
HOH
345
A
HOH
49
5
HOH
HOH
346
A
HOH
50
5
HOH
HOH
347
A
HOH
51
5
HOH
HOH
348
A
HOH
52
5
HOH
HOH
349
A
HOH
53
5
HOH
HOH
350
A
HOH
54
5
HOH
HOH
351
A
HOH
55
5
HOH
HOH
352
A
HOH
56
5
HOH
HOH
353
A
HOH
57
5
HOH
HOH
354
A
HOH
58
5
HOH
HOH
355
A
HOH
59
5
HOH
HOH
356
A
HOH
60
5
HOH
HOH
357
A
HOH
61
5
HOH
HOH
358
A
HOH
62
5
HOH
HOH
359
A
HOH
63
5
HOH
HOH
360
A
HOH
64
5
HOH
HOH
361
A
HOH
65
5
HOH
HOH
362
A
HOH
66
5
HOH
HOH
363
A
n
1
0
A
SER
1
n
2
SER
1
A
THR
2
n
3
THR
2
A
GLU
3
n
4
GLU
3
A
TYR
4
n
5
TYR
4
A
LYS
5
n
6
LYS
5
A
LEU
6
n
7
LEU
6
A
VAL
7
n
8
VAL
7
A
VAL
8
n
9
VAL
8
A
VAL
9
n
10
VAL
9
A
GLY
10
n
11
GLY
10
A
ALA
11
n
12
ALA
11
A
ASP
12
n
13
ASP
12
A
GLY
13
n
14
GLY
13
A
VAL
14
n
15
VAL
14
A
GLY
15
n
16
GLY
15
A
LYS
16
n
17
LYS
16
A
SER
17
n
18
SER
17
A
ALA
18
n
19
ALA
18
A
LEU
19
n
20
LEU
19
A
THR
20
n
21
THR
20
A
ILE
21
n
22
ILE
21
A
GLN
22
n
23
GLN
22
A
LEU
23
n
24
LEU
23
A
ILE
24
n
25
ILE
24
A
GLN
25
n
26
GLN
25
A
ASN
26
n
27
ASN
26
A
HIS
27
n
28
HIS
27
A
PHE
28
n
29
PHE
28
A
VAL
29
n
30
VAL
29
A
ASP
30
n
31
ASP
30
A
GLU
31
n
32
GLU
31
A
TYR
32
n
33
TYR
32
A
ASP
33
n
34
ASP
33
A
PRO
34
n
35
PRO
34
A
THR
35
n
36
THR
35
A
ILE
36
n
37
ILE
36
A
GLU
37
n
38
GLU
37
A
ASP
38
n
39
ASP
38
A
SER
39
n
40
SER
39
A
TYR
40
n
41
TYR
40
A
ARG
41
n
42
ARG
41
A
LYS
42
n
43
LYS
42
A
GLN
43
n
44
GLN
43
A
VAL
44
n
45
VAL
44
A
VAL
45
n
46
VAL
45
A
ILE
46
n
47
ILE
46
A
ASP
47
n
48
ASP
47
A
GLY
48
n
49
GLY
48
A
GLU
49
n
50
GLU
49
A
THR
50
n
51
THR
50
A
CYS
51
n
52
CYS
51
A
LEU
52
n
53
LEU
52
A
LEU
53
n
54
LEU
53
A
ASP
54
n
55
ASP
54
A
ILE
55
n
56
ILE
55
A
LEU
56
n
57
LEU
56
A
ASP
57
n
58
ASP
57
A
THR
58
n
59
THR
58
A
ALA
59
n
60
ALA
59
A
GLY
60
n
61
GLY
60
A
GLN
61
n
62
GLN
61
A
n
63
62
A
n
64
63
A
n
65
64
A
SER
65
n
66
SER
65
A
ALA
66
n
67
ALA
66
A
MET
67
n
68
MET
67
A
ARG
68
n
69
ARG
68
A
ASP
69
n
70
ASP
69
A
GLN
70
n
71
GLN
70
A
TYR
71
n
72
TYR
71
A
MET
72
n
73
MET
72
A
ARG
73
n
74
ARG
73
A
THR
74
n
75
THR
74
A
GLY
75
n
76
GLY
75
A
GLU
76
n
77
GLU
76
A
GLY
77
n
78
GLY
77
A
PHE
78
n
79
PHE
78
A
LEU
79
n
80
LEU
79
A
CYS
80
n
81
CYS
80
A
VAL
81
n
82
VAL
81
A
PHE
82
n
83
PHE
82
A
ALA
83
n
84
ALA
83
A
ILE
84
n
85
ILE
84
A
ASN
85
n
86
ASN
85
A
ASN
86
n
87
ASN
86
A
THR
87
n
88
THR
87
A
LYS
88
n
89
LYS
88
A
SER
89
n
90
SER
89
A
PHE
90
n
91
PHE
90
A
GLU
91
n
92
GLU
91
A
ASP
92
n
93
ASP
92
A
ILE
93
n
94
ILE
93
A
HIS
94
n
95
HIS
94
A
HIS
95
n
96
HIS
95
A
TYR
96
n
97
TYR
96
A
ARG
97
n
98
ARG
97
A
GLU
98
n
99
GLU
98
A
GLN
99
n
100
GLN
99
A
ILE
100
n
101
ILE
100
A
LYS
101
n
102
LYS
101
A
ARG
102
n
103
ARG
102
A
VAL
103
n
104
VAL
103
A
LYS
104
n
105
LYS
104
A
ASP
105
n
106
ASP
105
A
SER
106
n
107
SER
106
A
GLU
107
n
108
GLU
107
A
ASP
108
n
109
ASP
108
A
VAL
109
n
110
VAL
109
A
PRO
110
n
111
PRO
110
A
MET
111
n
112
MET
111
A
VAL
112
n
113
VAL
112
A
LEU
113
n
114
LEU
113
A
VAL
114
n
115
VAL
114
A
GLY
115
n
116
GLY
115
A
ASN
116
n
117
ASN
116
A
LYS
117
n
118
LYS
117
A
CYS
118
n
119
CYS
118
A
ASP
119
n
120
ASP
119
A
LEU
120
n
121
LEU
120
A
PRO
121
n
122
PRO
121
A
SER
122
n
123
SER
122
A
ARG
123
n
124
ARG
123
A
THR
124
n
125
THR
124
A
VAL
125
n
126
VAL
125
A
ASP
126
n
127
ASP
126
A
THR
127
n
128
THR
127
A
LYS
128
n
129
LYS
128
A
GLN
129
n
130
GLN
129
A
ALA
130
n
131
ALA
130
A
GLN
131
n
132
GLN
131
A
ASP
132
n
133
ASP
132
A
LEU
133
n
134
LEU
133
A
ALA
134
n
135
ALA
134
A
ARG
135
n
136
ARG
135
A
SER
136
n
137
SER
136
A
TYR
137
n
138
TYR
137
A
GLY
138
n
139
GLY
138
A
ILE
139
n
140
ILE
139
A
PRO
140
n
141
PRO
140
A
PHE
141
n
142
PHE
141
A
ILE
142
n
143
ILE
142
A
GLU
143
n
144
GLU
143
A
THR
144
n
145
THR
144
A
SER
145
n
146
SER
145
A
ALA
146
n
147
ALA
146
A
LYS
147
n
148
LYS
147
A
THR
148
n
149
THR
148
A
ARG
149
n
150
ARG
149
A
GLN
150
n
151
GLN
150
A
GLY
151
n
152
GLY
151
A
VAL
152
n
153
VAL
152
A
ASP
153
n
154
ASP
153
A
ASP
154
n
155
ASP
154
A
ALA
155
n
156
ALA
155
A
PHE
156
n
157
PHE
156
A
TYR
157
n
158
TYR
157
A
THR
158
n
159
THR
158
A
LEU
159
n
160
LEU
159
A
VAL
160
n
161
VAL
160
A
ARG
161
n
162
ARG
161
A
GLU
162
n
163
GLU
162
A
ILE
163
n
164
ILE
163
A
ARG
164
n
165
ARG
164
A
LYS
165
n
166
LYS
165
A
HIS
166
n
167
HIS
166
A
LYS
167
n
168
LYS
167
A
GLU
168
n
169
GLU
168
A
LYS
169
n
170
LYS
169
A
MET
170
n
171
MET
170
A
SER
171
n
172
SER
171
A
LYS
172
n
173
LYS
172
A
ASP
173
n
174
ASP
173
A
GLY
174
n
175
GLY
174
A
LYS
175
n
176
LYS
175
A
LYS
176
n
177
LYS
176
A
LYS
177
n
178
LYS
177
A
LYS
178
n
179
LYS
178
A
LYS
179
n
180
LYS
179
A
LYS
180
n
181
LYS
180
A
n
182
181
A
n
183
182
A
n
184
183
A
n
185
184
A
n
186
185
A
n
187
186
A
n
188
187
A
n
189
188
A
author_and_software_defined_assembly
PISA
1
monomeric
A
SER
17
A
OG
SER
18
1_555
A
MG
202
C
MG
MG
1_555
A
GDP
201
B
O3B
GDP
1_555
91.8
A
SER
17
A
OG
SER
18
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
304
E
O
HOH
1_555
85.2
A
GDP
201
B
O3B
GDP
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
304
E
O
HOH
1_555
90.6
A
SER
17
A
OG
SER
18
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
305
E
O
HOH
1_555
89.6
A
GDP
201
B
O3B
GDP
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
305
E
O
HOH
1_555
91.2
A
HOH
304
E
O
HOH
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
305
E
O
HOH
1_555
174.5
A
SER
17
A
OG
SER
18
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
309
E
O
HOH
1_555
88.5
A
GDP
201
B
O3B
GDP
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
309
E
O
HOH
1_555
178.9
A
HOH
304
E
O
HOH
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
309
E
O
HOH
1_555
90.5
A
HOH
305
E
O
HOH
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
309
E
O
HOH
1_555
87.7
A
SER
17
A
OG
SER
18
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
346
E
O
HOH
1_555
171.9
A
GDP
201
B
O3B
GDP
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
346
E
O
HOH
1_555
92.6
A
HOH
304
E
O
HOH
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
346
E
O
HOH
1_555
88.0
A
HOH
305
E
O
HOH
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
346
E
O
HOH
1_555
97.0
A
HOH
309
E
O
HOH
1_555
A
MG
202
C
MG
MG
1_555
A
HOH
346
E
O
HOH
1_555
87.2
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
N
VAL
44
A
N
VAL
45
A
O
CYS
51
A
O
CYS
52
A
O
LEU
56
A
O
LEU
57
A
N
VAL
8
A
N
VAL
9
A
N
VAL
9
A
N
VAL
10
A
O
VAL
81
A
O
VAL
82
A
N
PHE
82
A
N
PHE
83
A
O
ASN
116
A
O
ASN
117
A
N
LEU
113
A
N
LEU
114
A
O
ILE
142
A
O
ILE
143
1
A
HOH
301
E
HOH
1
A
CG
LYS
175
A
CG
LYS
176
1
Y
1
A
CD
LYS
175
A
CD
LYS
176
1
Y
1
A
CE
LYS
175
A
CE
LYS
176
1
Y
1
A
NZ
LYS
175
A
NZ
LYS
176
1
Y
1
A
CG
LYS
176
A
CG
LYS
177
1
Y
1
A
CD
LYS
176
A
CD
LYS
177
1
Y
1
A
CE
LYS
176
A
CE
LYS
177
1
Y
1
A
NZ
LYS
176
A
NZ
LYS
177
1
Y
1
A
CG
LYS
177
A
CG
LYS
178
1
Y
1
A
CD
LYS
177
A
CD
LYS
178
1
Y
1
A
CE
LYS
177
A
CE
LYS
178
1
Y
1
A
NZ
LYS
177
A
NZ
LYS
178
1
Y
1
A
CG
LYS
178
A
CG
LYS
179
1
Y
1
A
CD
LYS
178
A
CD
LYS
179
1
Y
1
A
CE
LYS
178
A
CE
LYS
179
1
Y
1
A
NZ
LYS
178
A
NZ
LYS
179
1
Y
1
A
CG
LYS
179
A
CG
LYS
180
1
Y
1
A
CD
LYS
179
A
CD
LYS
180
1
Y
1
A
CE
LYS
179
A
CE
LYS
180
1
Y
1
A
NZ
LYS
179
A
NZ
LYS
180
1
Y
1
A
CG
LYS
180
A
CG
LYS
181
1
Y
1
A
CD
LYS
180
A
CD
LYS
181
1
Y
1
A
CE
LYS
180
A
CE
LYS
181
1
Y
1
A
NZ
LYS
180
A
NZ
LYS
181
1
Y
1
A
GLY
0
A
GLY
1
1
Y
1
A
GLU
62
A
GLU
63
1
Y
1
A
GLU
63
A
GLU
64
1
Y
1
A
TYR
64
A
TYR
65
1
Y
1
A
SER
181
A
SER
182
1
Y
1
A
LYS
182
A
LYS
183
1
Y
1
A
THR
183
A
THR
184
1
Y
1
A
LYS
184
A
LYS
185
1
Y
1
A
CYS
185
A
CYS
186
1
Y
1
A
VAL
186
A
VAL
187
1
Y
1
A
ILE
187
A
ILE
188
1
Y
1
A
MET
188
A
MET
189
1
Y
1
A
GLU
31
-63.69
-150.73
1
A
TYR
32
174.42
152.58
1
A
ASP
33
-176.06
81.50
1
A
LYS
117
72.94
33.72
1
A
ARG
149
82.51
-0.08
1
A
ASP
173
41.02
-164.05
1
A
LYS
176
78.73
-52.71
1
A
LYS
177
-129.46
-56.75
1
A
LYS
178
71.67
172.15
1
A
LYS
179
-156.88
-85.03
-1.8021
-0.0000
0.0000
-1.8021
-0.0000
3.6042
0.2028
0.1597
0.162
0.1619
1.7
26.018
1028
21312
20284
5.07
99.92
0.19
RANDOM
1
1.98
MOLECULAR REPLACEMENT
17.45
0.90
1.11
ML
FLAT BULK SOLVENT MODEL
59.342
0.400
1.7
26.018
63
1488
38
0
1387
0.006
1447
0.959
1956
14.881
540
0.064
219
0.004
251
0.2176
0.1662
1.7881
133
2737
100.00
0.1994
0.1321
1.9001
145
2759
100.00
0.1842
0.1180
2.0467
142
2773
100.00
0.2128
0.1284
2.2526
144
2746
100.00
0.2069
0.1422
2.5783
161
2763
100.00
0.2319
0.1580
3.2474
149
2735
100.00
0.1905
0.1807
26.0214
154
2743
99.00
29.7
1.7
500
4DSU
20451
20431
1
1
0.046
1
26.7
4.6
99.9
1.70
1.76
3.2
2010
0.455
1
4.6
100
data collection
BOS
phasing
PHASER
refinement
PHENIX
(phenix.refine: 1.6.4_486)
data reduction
HKL-2000
data scaling
SCALEPACK
Small-molecule ligands bind to a distinct pocket in Ras and inhibit SOS-mediated nucleotide exchange activity
1
N
N
2
N
N
3
N
N
4
N
N
5
N
N
A
GLY
15
A
GLY
16
HELX_P
A
ASN
26
A
ASN
27
1
1
12
A
MET
67
A
MET
68
HELX_P
A
GLY
75
A
GLY
76
1
2
9
A
ASN
86
A
ASN
87
HELX_P
A
LYS
104
A
LYS
105
1
3
19
A
ASP
126
A
ASP
127
HELX_P
A
GLY
138
A
GLY
139
1
4
13
A
GLY
151
A
GLY
152
HELX_P
A
ASP
173
A
ASP
174
1
5
23
metalc
2.225
A
SER
17
A
OG
SER
18
1_555
A
MG
202
C
MG
MG
1_555
metalc
2.133
A
GDP
201
B
O3B
GDP
1_555
A
MG
202
C
MG
MG
1_555
metalc
2.277
A
MG
202
C
MG
MG
1_555
A
HOH
304
E
O
HOH
1_555
metalc
2.288
A
MG
202
C
MG
MG
1_555
A
HOH
305
E
O
HOH
1_555
metalc
2.280
A
MG
202
C
MG
MG
1_555
A
HOH
309
E
O
HOH
1_555
metalc
2.324
A
MG
202
C
MG
MG
1_555
A
HOH
346
E
O
HOH
1_555
HYDROLASE
small G-protein, signaling, Hydrolase
RASK_HUMAN
UNP
1
2
P01116
TEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQYMRTGEGFLCV
FAINNTKSFEDIHHYREQIKRVKDSEDVPMVLVGNKCDLPSRTVDTKQAQDLARSYGIPFIETSAKTRQGVDDAFYTLVR
EIRKHKEKMSKDGKKKKKKSKTKCVIM
2
188
4DSU
2
188
P01116
A
1
3
189
1
expression tag
GLY
0
4DSU
A
P01116
UNP
1
1
expression tag
SER
1
4DSU
A
P01116
UNP
2
1
GLY
engineered mutation
ASP
12
4DSU
A
P01116
UNP
12
13
6
anti-parallel
parallel
parallel
parallel
parallel
A
ASP
38
A
ASP
39
A
ILE
46
A
ILE
47
A
GLU
49
A
GLU
50
A
ASP
57
A
ASP
58
A
THR
2
A
THR
3
A
VAL
9
A
VAL
10
A
GLY
77
A
GLY
78
A
ALA
83
A
ALA
84
A
MET
111
A
MET
112
A
ASN
116
A
ASN
117
A
PHE
141
A
PHE
142
A
GLU
143
A
GLU
144
BINDING SITE FOR RESIDUE GDP A 201
A
GDP
201
Software
24
BINDING SITE FOR RESIDUE MG A 202
A
MG
202
Software
6
BINDING SITE FOR RESIDUE BZI A 203
A
BZI
203
Software
5
A
GLY
13
A
GLY
14
24
1_555
A
VAL
14
A
VAL
15
24
1_555
A
GLY
15
A
GLY
16
24
1_555
A
LYS
16
A
LYS
17
24
1_555
A
SER
17
A
SER
18
24
1_555
A
ALA
18
A
ALA
19
24
1_555
A
PHE
28
A
PHE
29
24
1_555
A
VAL
29
A
VAL
30
24
1_555
A
ASP
30
A
ASP
31
24
1_555
A
GLU
31
A
GLU
32
24
1_555
A
ASN
116
A
ASN
117
24
1_555
A
LYS
117
A
LYS
118
24
1_555
A
ASP
119
A
ASP
120
24
1_555
A
LEU
120
A
LEU
121
24
1_555
A
SER
145
A
SER
146
24
1_555
A
ALA
146
A
ALA
147
24
1_555
A
LYS
147
A
LYS
148
24
1_555
A
MG
202
C
MG
24
1_555
A
HOH
305
E
HOH
24
1_555
A
HOH
308
E
HOH
24
3_555
A
HOH
323
E
HOH
24
1_555
A
HOH
327
E
HOH
24
1_555
A
HOH
332
E
HOH
24
1_555
A
HOH
346
E
HOH
24
1_555
A
SER
17
A
SER
18
6
1_555
A
GDP
201
B
GDP
6
1_555
A
HOH
304
E
HOH
6
1_555
A
HOH
305
E
HOH
6
1_555
A
HOH
309
E
HOH
6
1_555
A
HOH
346
E
HOH
6
1_555
A
LYS
5
A
LYS
6
5
1_555
A
LEU
6
A
LEU
7
5
1_555
A
VAL
7
A
VAL
8
5
1_555
A
ASP
54
A
ASP
55
5
1_555
A
HOH
361
E
HOH
5
1_555
146
H 3