0.029404
0.000000
0.000000
0.000000
0.014913
0.000000
0.000000
0.000000
0.014749
0.00000
0.00000
0.00000
Komander, D.
Bayascas, J.R.
Deak, M.
Alessi, D.R.
van Aalten, D.M.F.
http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic
4
90.00
90.00
90.00
34.009
67.057
67.802
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
C3 H8 O3
92.094
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
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
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
O4 S -2
96.063
SULFATE ION
non-polymer
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
C
N
138
N
O
N
139
N
C
N
140
N
O
N
141
N
C
N
142
N
O
N
143
N
H
N
144
N
H
N
145
N
H
N
146
N
H
N
147
N
H
N
148
N
H
N
149
N
H
N
150
N
H
N
151
N
N
N
152
S
C
N
153
N
C
N
154
N
O
N
155
N
C
Y
156
N
C
Y
157
N
N
Y
158
N
C
Y
159
N
C
Y
160
N
N
N
161
N
O
N
162
N
H
N
163
N
H
N
164
N
H
N
165
N
H
N
166
N
H
N
167
N
H
N
168
N
H
N
169
N
H
N
170
N
H
N
171
N
H
N
172
N
O
N
173
N
H
N
174
N
H
N
175
N
N
N
176
S
C
N
177
N
C
N
178
N
O
N
179
S
C
N
180
N
C
N
181
N
C
N
182
N
C
N
183
N
O
N
184
N
H
N
185
N
H
N
186
N
H
N
187
N
H
N
188
N
H
N
189
N
H
N
190
N
H
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
N
N
198
S
C
N
199
N
C
N
200
N
O
N
201
N
C
N
202
N
C
N
203
N
C
N
204
N
C
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
H
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
N
C
N
224
N
C
N
225
N
C
N
226
N
C
N
227
N
N
N
228
N
O
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
H
N
242
N
H
N
243
N
H
N
244
N
N
N
245
S
C
N
246
N
C
N
247
N
O
N
248
N
C
N
249
N
C
N
250
N
S
N
251
N
C
N
252
N
O
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
H
N
264
N
N
N
265
S
C
N
266
N
C
N
267
N
O
N
268
N
C
Y
269
N
C
Y
270
N
C
Y
271
N
C
Y
272
N
C
Y
273
N
C
Y
274
N
C
N
275
N
O
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
N
N
288
S
C
N
289
N
C
N
290
N
O
N
291
N
C
N
292
N
C
N
293
N
C
N
294
N
O
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
N
N
305
S
C
N
306
N
C
N
307
N
O
N
308
N
C
N
309
N
O
N
310
N
O
N
311
N
H
N
312
N
H
N
313
N
H
N
314
N
H
N
315
N
H
N
316
N
H
N
317
N
H
N
318
N
S
N
319
N
O
N
320
N
O
N
321
N
O
N
322
N
O
N
323
N
N
N
324
S
C
N
325
N
C
N
326
N
O
N
327
R
C
N
328
N
O
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
Y
345
N
C
Y
346
N
C
Y
347
N
C
Y
348
N
N
Y
349
N
C
Y
350
N
C
Y
351
N
C
Y
352
N
C
Y
353
N
C
N
354
N
O
N
355
N
H
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
H
N
364
N
H
N
365
N
H
N
366
N
H
N
367
N
N
N
368
S
C
N
369
N
C
N
370
N
O
N
371
N
C
Y
372
N
C
Y
373
N
C
Y
374
N
C
Y
375
N
C
Y
376
N
C
Y
377
N
C
N
378
N
O
N
379
N
O
N
380
N
H
N
381
N
H
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
C
N
397
N
C
N
398
N
O
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
H
N
408
N
H
N
409
N
H
N
1
N
sing
N
2
N
sing
N
3
N
sing
N
4
N
sing
N
5
N
sing
N
6
N
sing
N
7
N
doub
N
8
N
sing
N
9
N
sing
N
10
N
sing
N
11
N
sing
N
12
N
sing
N
13
N
sing
N
14
N
sing
N
15
N
sing
N
16
N
sing
N
17
N
sing
N
18
N
sing
N
19
N
doub
N
20
N
sing
N
21
N
sing
N
22
N
sing
N
23
N
sing
N
24
N
sing
N
25
N
sing
N
26
N
sing
N
27
N
sing
N
28
N
sing
N
29
N
sing
N
30
N
sing
N
31
N
sing
N
32
N
sing
N
33
N
doub
N
34
N
sing
N
35
N
sing
N
36
N
sing
N
37
N
sing
N
38
N
sing
N
39
N
sing
N
40
N
sing
N
41
N
sing
N
42
N
sing
N
43
N
sing
N
44
N
sing
N
45
N
doub
N
46
N
sing
N
47
N
sing
N
48
N
sing
N
49
N
sing
N
50
N
doub
N
51
N
sing
N
52
N
sing
N
53
N
sing
N
54
N
sing
N
55
N
sing
N
56
N
sing
N
57
N
sing
N
58
N
sing
N
59
N
sing
N
60
N
sing
N
61
N
doub
N
62
N
sing
N
63
N
sing
N
64
N
sing
N
65
N
sing
N
66
N
doub
N
67
N
sing
N
68
N
sing
N
69
N
sing
N
70
N
sing
N
71
N
sing
N
72
N
sing
N
73
N
sing
N
74
N
sing
N
75
N
sing
N
76
N
doub
N
77
N
sing
N
78
N
sing
N
79
N
sing
N
80
N
sing
N
81
N
sing
N
82
N
sing
N
83
N
sing
N
84
N
sing
N
85
N
sing
N
86
N
sing
N
87
N
sing
N
88
N
sing
N
89
N
doub
N
90
N
sing
N
91
N
sing
N
92
N
sing
N
93
N
sing
N
94
N
sing
N
95
N
sing
N
96
N
sing
N
97
N
doub
N
98
N
sing
N
99
N
sing
N
100
N
sing
N
101
N
sing
N
102
N
sing
N
103
N
sing
N
104
N
sing
N
105
N
sing
N
106
N
sing
N
107
N
sing
N
108
N
doub
N
109
N
sing
N
110
N
sing
N
111
N
sing
N
112
N
sing
N
113
N
sing
N
114
N
sing
N
115
N
sing
N
116
N
doub
N
117
N
sing
N
118
N
sing
N
119
N
sing
N
120
N
sing
N
121
N
sing
N
122
N
sing
N
123
N
sing
N
124
N
sing
N
125
N
sing
N
126
N
doub
N
127
N
sing
N
128
N
sing
N
129
N
sing
N
130
N
sing
N
131
N
sing
N
132
N
sing
N
133
N
sing
N
134
N
sing
N
135
N
sing
N
136
N
sing
N
137
N
sing
N
138
N
sing
N
139
N
sing
N
140
N
sing
N
141
N
sing
N
142
N
sing
N
143
N
sing
N
144
N
sing
N
145
N
sing
N
146
N
sing
N
147
N
sing
N
148
N
doub
N
149
N
sing
N
150
N
sing
N
151
N
sing
N
152
N
sing
Y
153
N
sing
Y
154
N
doub
Y
155
N
doub
N
156
N
sing
Y
157
N
sing
N
158
N
sing
Y
159
N
sing
N
160
N
sing
N
161
N
sing
N
162
N
sing
N
163
N
sing
N
164
N
sing
N
165
N
sing
N
166
N
sing
N
167
N
sing
N
168
N
sing
N
169
N
sing
N
170
N
sing
N
171
N
doub
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
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
doub
N
193
N
sing
N
194
N
sing
N
195
N
sing
N
196
N
sing
N
197
N
sing
N
198
N
sing
N
199
N
sing
N
200
N
sing
N
201
N
sing
N
202
N
sing
N
203
N
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
doub
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
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
doub
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
sing
N
252
N
sing
N
253
N
sing
N
254
N
sing
N
255
N
sing
N
256
N
doub
N
257
N
sing
N
258
N
sing
N
259
N
sing
N
260
N
sing
Y
261
N
doub
Y
262
N
sing
Y
263
N
sing
N
264
N
sing
Y
265
N
doub
N
266
N
sing
Y
267
N
doub
N
268
N
sing
Y
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
doub
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
sing
N
295
N
sing
N
296
N
doub
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
doub
N
304
N
doub
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
doub
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
doub
N
330
N
sing
N
331
N
sing
N
332
N
sing
N
333
N
sing
Y
334
N
doub
Y
335
N
sing
Y
336
N
sing
N
337
N
sing
Y
338
N
doub
Y
339
N
sing
Y
340
N
sing
N
341
N
sing
Y
342
N
sing
Y
343
N
doub
N
344
N
sing
Y
345
N
doub
N
346
N
sing
Y
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
Y
362
N
doub
Y
363
N
sing
Y
364
N
sing
N
365
N
sing
Y
366
N
doub
N
367
N
sing
Y
368
N
doub
N
369
N
sing
Y
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
doub
N
382
N
sing
N
383
N
sing
N
384
N
sing
N
385
N
sing
N
386
N
sing
N
387
N
sing
N
388
N
sing
N
389
N
sing
N
390
N
sing
N
391
N
sing
N
392
N
sing
US
Mol.Cell.Biol.
MCEBD4
2044
0270-7306
28
3258
10.1128/MCB.02032-07
18347057
Mutation of the Pdk1 Ph Domain Inhibits Protein Kinase B/Akt, Leading to Small Size and Insulin Resistance.
2008
10.2210/pdb2vki/pdb
pdb_00002vki
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
1
IMAGE PLATE
2004-06-30
RIGAKU IMAGE PLATE
SINGLE WAVELENGTH
M
x-ray
1
1.5418
1.0
1.5418
ROTATING ANODE
RIGAKU MICROMAX-007
17548.791
3-PHOPSHOINOSITIDE DEPENDENT PROTEIN KINASE 1
2.7.11.1
PLECKSTRIN HOMOLOGY (PH) DOMAIN, RESIDUES 409-556
YES
1
man
polymer
92.094
GLYCEROL
1
syn
non-polymer
96.063
SULFATE ION
1
syn
non-polymer
18.015
water
112
nat
water
HPDK1
no
no
GSNIEQYIHDLDSNSFELDLQFSEDEKRLLLEKQAGGNPWHQFVENNLILKMGPVDERKGLFARRRQLLLTEGPHLYYVD
PVNKVLKGEIPWSQELRPEAKNFKTFFVHTPNRTYYLMDPSGNAHKWCRKIQEVWRQRYQSHPDAAVQ
GSNIEQYIHDLDSNSFELDLQFSEDEKRLLLEKQAGGNPWHQFVENNLILKMGPVDERKGLFARRRQLLLTEGPHLYYVD
PVNKVLKGEIPWSQELRPEAKNFKTFFVHTPNRTYYLMDPSGNAHKWCRKIQEVWRQRYQSHPDAAVQ
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
HUMAN
sample
9606
HOMO SAPIENS
469008
ESCHERICHIA COLI
BL21(DE3)
PGEX6P1
1
2.2
44
NONE
8.5
0.2 M LITHIUM SULPHATE, 0.1 M TRIS HYDROCHLORIDE [PH 8.5] 30 % (W/V) PEG 4000
chem_comp_atom
chem_comp_bond
database_2
pdbx_database_status
pdbx_initial_refinement_model
repository
Initial release
Advisory
Refinement description
Version format compliance
Data collection
Database references
Other
Refinement description
1
0
2008-05-13
1
1
2011-07-13
1
2
2023-12-13
_database_2.pdbx_DOI
_database_2.pdbx_database_accession
_pdbx_database_status.status_code_sf
STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-1
STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH STAUROSPORINE
CRYSTAL STRUCTURE OF N1-[3-[[5-BROMO-2-[[ 3-[(1-PYRROLIDINYLCARBONYL)AMINO]PHENYL]AMINO ]-4-PYRIMIDINYL]AMINO]PROPYL]-2,2- DIMETHYLPROPANEDIAMIDECOMPLEXED WITH HUMAN PDK1
STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-3
STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH UCN-01
CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN BOUND TO INOSITOL (1, 3,4,5)-TETRAKISPHOSPHATE
HIGH RESOLUTION CRYSTAL STRUCTURE OF THE HUMAN PDK1 CATALYTIC DOMAIN
STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH LY333531
CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN BOUND TO DIC4- PHOSPHATIDYLINOSITOL (3,4,5)-TRISPHOSPHATE
STRUCTURE OF PDK1-S241A MUTANT KINASE DOMAIN
CRYSTAL STRUCTURE OF THE PDK1 PLECKSTRIN HOMOLOGY (PH) DOMAIN
STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-2
STRUCTURE OF HUMAN PDK1 KINASE DOMAIN IN COMPLEX WITH BIM-8
SHEET
THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN
ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW,
TWO SHEETS ARE DEFINED.
PDBE
Y
PDBE
2007-12-19
REL
REL
GOL
GLYCEROL
SO4
SULFATE ION
HOH
water
ENGINEERED RESIDUE IN CHAIN A, LYS 465 TO GLU
POINT MUTATION K465E
1W1D
PDB ENTRY 1W1D
PDB
experimental model
GOL
1549
2
GOL
GOL
1549
A
SO4
1550
3
SO4
SO4
1550
A
HOH
2001
4
HOH
HOH
2001
A
HOH
2002
4
HOH
HOH
2002
A
HOH
2003
4
HOH
HOH
2003
A
HOH
2004
4
HOH
HOH
2004
A
HOH
2005
4
HOH
HOH
2005
A
HOH
2006
4
HOH
HOH
2006
A
HOH
2007
4
HOH
HOH
2007
A
HOH
2008
4
HOH
HOH
2008
A
HOH
2009
4
HOH
HOH
2009
A
HOH
2010
4
HOH
HOH
2010
A
HOH
2011
4
HOH
HOH
2011
A
HOH
2012
4
HOH
HOH
2012
A
HOH
2013
4
HOH
HOH
2013
A
HOH
2014
4
HOH
HOH
2014
A
HOH
2015
4
HOH
HOH
2015
A
HOH
2016
4
HOH
HOH
2016
A
HOH
2017
4
HOH
HOH
2017
A
HOH
2018
4
HOH
HOH
2018
A
HOH
2019
4
HOH
HOH
2019
A
HOH
2020
4
HOH
HOH
2020
A
HOH
2021
4
HOH
HOH
2021
A
HOH
2022
4
HOH
HOH
2022
A
HOH
2023
4
HOH
HOH
2023
A
HOH
2024
4
HOH
HOH
2024
A
HOH
2025
4
HOH
HOH
2025
A
HOH
2026
4
HOH
HOH
2026
A
HOH
2027
4
HOH
HOH
2027
A
HOH
2028
4
HOH
HOH
2028
A
HOH
2029
4
HOH
HOH
2029
A
HOH
2030
4
HOH
HOH
2030
A
HOH
2031
4
HOH
HOH
2031
A
HOH
2032
4
HOH
HOH
2032
A
HOH
2033
4
HOH
HOH
2033
A
HOH
2034
4
HOH
HOH
2034
A
HOH
2035
4
HOH
HOH
2035
A
HOH
2036
4
HOH
HOH
2036
A
HOH
2037
4
HOH
HOH
2037
A
HOH
2038
4
HOH
HOH
2038
A
HOH
2039
4
HOH
HOH
2039
A
HOH
2040
4
HOH
HOH
2040
A
HOH
2041
4
HOH
HOH
2041
A
HOH
2042
4
HOH
HOH
2042
A
HOH
2043
4
HOH
HOH
2043
A
HOH
2044
4
HOH
HOH
2044
A
HOH
2045
4
HOH
HOH
2045
A
HOH
2046
4
HOH
HOH
2046
A
HOH
2047
4
HOH
HOH
2047
A
HOH
2048
4
HOH
HOH
2048
A
HOH
2049
4
HOH
HOH
2049
A
HOH
2050
4
HOH
HOH
2050
A
HOH
2051
4
HOH
HOH
2051
A
HOH
2052
4
HOH
HOH
2052
A
HOH
2053
4
HOH
HOH
2053
A
HOH
2054
4
HOH
HOH
2054
A
HOH
2055
4
HOH
HOH
2055
A
HOH
2056
4
HOH
HOH
2056
A
HOH
2057
4
HOH
HOH
2057
A
HOH
2058
4
HOH
HOH
2058
A
HOH
2059
4
HOH
HOH
2059
A
HOH
2060
4
HOH
HOH
2060
A
HOH
2061
4
HOH
HOH
2061
A
HOH
2062
4
HOH
HOH
2062
A
HOH
2063
4
HOH
HOH
2063
A
HOH
2064
4
HOH
HOH
2064
A
HOH
2065
4
HOH
HOH
2065
A
HOH
2066
4
HOH
HOH
2066
A
HOH
2067
4
HOH
HOH
2067
A
HOH
2068
4
HOH
HOH
2068
A
HOH
2069
4
HOH
HOH
2069
A
HOH
2070
4
HOH
HOH
2070
A
HOH
2071
4
HOH
HOH
2071
A
HOH
2072
4
HOH
HOH
2072
A
HOH
2073
4
HOH
HOH
2073
A
HOH
2074
4
HOH
HOH
2074
A
HOH
2075
4
HOH
HOH
2075
A
HOH
2076
4
HOH
HOH
2076
A
HOH
2077
4
HOH
HOH
2077
A
HOH
2078
4
HOH
HOH
2078
A
HOH
2079
4
HOH
HOH
2079
A
HOH
2080
4
HOH
HOH
2080
A
HOH
2081
4
HOH
HOH
2081
A
HOH
2082
4
HOH
HOH
2082
A
HOH
2083
4
HOH
HOH
2083
A
HOH
2084
4
HOH
HOH
2084
A
HOH
2085
4
HOH
HOH
2085
A
HOH
2086
4
HOH
HOH
2086
A
HOH
2087
4
HOH
HOH
2087
A
HOH
2088
4
HOH
HOH
2088
A
HOH
2089
4
HOH
HOH
2089
A
HOH
2090
4
HOH
HOH
2090
A
HOH
2091
4
HOH
HOH
2091
A
HOH
2092
4
HOH
HOH
2092
A
HOH
2093
4
HOH
HOH
2093
A
HOH
2094
4
HOH
HOH
2094
A
HOH
2095
4
HOH
HOH
2095
A
HOH
2096
4
HOH
HOH
2096
A
HOH
2097
4
HOH
HOH
2097
A
HOH
2098
4
HOH
HOH
2098
A
HOH
2099
4
HOH
HOH
2099
A
HOH
2100
4
HOH
HOH
2100
A
HOH
2101
4
HOH
HOH
2101
A
HOH
2102
4
HOH
HOH
2102
A
HOH
2103
4
HOH
HOH
2103
A
HOH
2104
4
HOH
HOH
2104
A
HOH
2105
4
HOH
HOH
2105
A
HOH
2106
4
HOH
HOH
2106
A
HOH
2107
4
HOH
HOH
2107
A
HOH
2108
4
HOH
HOH
2108
A
HOH
2109
4
HOH
HOH
2109
A
HOH
2110
4
HOH
HOH
2110
A
HOH
2111
4
HOH
HOH
2111
A
HOH
2112
4
HOH
HOH
2112
A
n
1
409
A
SER
410
n
2
SER
410
A
ASN
411
n
3
ASN
411
A
ILE
412
n
4
ILE
412
A
GLU
413
n
5
GLU
413
A
GLN
414
n
6
GLN
414
A
TYR
415
n
7
TYR
415
A
ILE
416
n
8
ILE
416
A
HIS
417
n
9
HIS
417
A
ASP
418
n
10
ASP
418
A
LEU
419
n
11
LEU
419
A
ASP
420
n
12
ASP
420
A
SER
421
n
13
SER
421
A
ASN
422
n
14
ASN
422
A
SER
423
n
15
SER
423
A
PHE
424
n
16
PHE
424
A
GLU
425
n
17
GLU
425
A
LEU
426
n
18
LEU
426
A
ASP
427
n
19
ASP
427
A
LEU
428
n
20
LEU
428
A
GLN
429
n
21
GLN
429
A
PHE
430
n
22
PHE
430
A
SER
431
n
23
SER
431
A
GLU
432
n
24
GLU
432
A
ASP
433
n
25
ASP
433
A
GLU
434
n
26
GLU
434
A
LYS
435
n
27
LYS
435
A
ARG
436
n
28
ARG
436
A
LEU
437
n
29
LEU
437
A
LEU
438
n
30
LEU
438
A
LEU
439
n
31
LEU
439
A
GLU
440
n
32
GLU
440
A
LYS
441
n
33
LYS
441
A
GLN
442
n
34
GLN
442
A
ALA
443
n
35
ALA
443
A
GLY
444
n
36
GLY
444
A
GLY
445
n
37
GLY
445
A
ASN
446
n
38
ASN
446
A
PRO
447
n
39
PRO
447
A
TRP
448
n
40
TRP
448
A
HIS
449
n
41
HIS
449
A
GLN
450
n
42
GLN
450
A
PHE
451
n
43
PHE
451
A
VAL
452
n
44
VAL
452
A
GLU
453
n
45
GLU
453
A
ASN
454
n
46
ASN
454
A
ASN
455
n
47
ASN
455
A
LEU
456
n
48
LEU
456
A
ILE
457
n
49
ILE
457
A
LEU
458
n
50
LEU
458
A
LYS
459
n
51
LYS
459
A
MET
460
n
52
MET
460
A
GLY
461
n
53
GLY
461
A
PRO
462
n
54
PRO
462
A
VAL
463
n
55
VAL
463
A
ASP
464
n
56
ASP
464
A
GLU
465
n
57
GLU
465
A
ARG
466
n
58
ARG
466
A
LYS
467
n
59
LYS
467
A
GLY
468
n
60
GLY
468
A
LEU
469
n
61
LEU
469
A
PHE
470
n
62
PHE
470
A
ALA
471
n
63
ALA
471
A
ARG
472
n
64
ARG
472
A
ARG
473
n
65
ARG
473
A
ARG
474
n
66
ARG
474
A
GLN
475
n
67
GLN
475
A
LEU
476
n
68
LEU
476
A
LEU
477
n
69
LEU
477
A
LEU
478
n
70
LEU
478
A
THR
479
n
71
THR
479
A
GLU
480
n
72
GLU
480
A
GLY
481
n
73
GLY
481
A
PRO
482
n
74
PRO
482
A
HIS
483
n
75
HIS
483
A
LEU
484
n
76
LEU
484
A
TYR
485
n
77
TYR
485
A
TYR
486
n
78
TYR
486
A
VAL
487
n
79
VAL
487
A
ASP
488
n
80
ASP
488
A
PRO
489
n
81
PRO
489
A
VAL
490
n
82
VAL
490
A
ASN
491
n
83
ASN
491
A
LYS
492
n
84
LYS
492
A
VAL
493
n
85
VAL
493
A
LEU
494
n
86
LEU
494
A
LYS
495
n
87
LYS
495
A
GLY
496
n
88
GLY
496
A
GLU
497
n
89
GLU
497
A
ILE
498
n
90
ILE
498
A
PRO
499
n
91
PRO
499
A
TRP
500
n
92
TRP
500
A
SER
501
n
93
SER
501
A
GLN
502
n
94
GLN
502
A
GLU
503
n
95
GLU
503
A
LEU
504
n
96
LEU
504
A
ARG
505
n
97
ARG
505
A
PRO
506
n
98
PRO
506
A
GLU
507
n
99
GLU
507
A
ALA
508
n
100
ALA
508
A
LYS
509
n
101
LYS
509
A
ASN
510
n
102
ASN
510
A
PHE
511
n
103
PHE
511
A
LYS
512
n
104
LYS
512
A
THR
513
n
105
THR
513
A
PHE
514
n
106
PHE
514
A
PHE
515
n
107
PHE
515
A
VAL
516
n
108
VAL
516
A
HIS
517
n
109
HIS
517
A
THR
518
n
110
THR
518
A
PRO
519
n
111
PRO
519
A
ASN
520
n
112
ASN
520
A
ARG
521
n
113
ARG
521
A
THR
522
n
114
THR
522
A
TYR
523
n
115
TYR
523
A
TYR
524
n
116
TYR
524
A
LEU
525
n
117
LEU
525
A
MET
526
n
118
MET
526
A
ASP
527
n
119
ASP
527
A
PRO
528
n
120
PRO
528
A
SER
529
n
121
SER
529
A
GLY
530
n
122
GLY
530
A
ASN
531
n
123
ASN
531
A
ALA
532
n
124
ALA
532
A
HIS
533
n
125
HIS
533
A
LYS
534
n
126
LYS
534
A
TRP
535
n
127
TRP
535
A
CYS
536
n
128
CYS
536
A
ARG
537
n
129
ARG
537
A
LYS
538
n
130
LYS
538
A
ILE
539
n
131
ILE
539
A
GLN
540
n
132
GLN
540
A
GLU
541
n
133
GLU
541
A
VAL
542
n
134
VAL
542
A
TRP
543
n
135
TRP
543
A
ARG
544
n
136
ARG
544
A
GLN
545
n
137
GLN
545
A
ARG
546
n
138
ARG
546
A
TYR
547
n
139
TYR
547
A
GLN
548
n
140
GLN
548
A
SER
549
n
141
SER
549
A
n
142
550
A
n
143
551
A
n
144
552
A
n
145
553
A
n
146
554
A
n
147
555
A
n
148
556
A
0.3314
-0.1515
0.1228
1.1483
-0.1352
0.8004
-0.0030
-0.0485
-0.0011
0.0306
0.0445
-0.0373
-0.0251
0.0218
-0.0415
0.0395
-0.0056
-0.0072
0.0345
-0.0087
0.0428
refined
1.9703
17.6963
11.1860
X-RAY DIFFRACTION
0.5356
-0.2601
0.1261
0.2234
-0.0010
1.0095
-0.0394
-0.0679
0.0286
0.0022
0.0407
0.0228
0.0028
-0.0211
-0.0013
0.0117
0.0080
-0.0076
0.0128
-0.0209
0.0388
refined
-0.7469
16.3049
12.3078
X-RAY DIFFRACTION
A
414
A
466
X-RAY DIFFRACTION
1
A
472
A
487
X-RAY DIFFRACTION
1
A
494
A
543
X-RAY DIFFRACTION
1
A
410
A
413
X-RAY DIFFRACTION
2
A
467
A
471
X-RAY DIFFRACTION
2
A
544
A
549
X-RAY DIFFRACTION
2
A
488
A
493
X-RAY DIFFRACTION
2
author_and_software_defined_assembly
PISA
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
N
LEU
419
A
N
LEU
11
A
O
SER
423
A
O
SER
15
A
N
LEU
426
A
N
LEU
18
A
O
LEU
458
A
O
LEU
50
A
N
GLU
465
A
N
GLU
57
A
O
ARG
472
A
O
ARG
64
A
N
THR
479
A
N
THR
71
A
O
HIS
483
A
O
HIS
75
A
N
ASP
488
A
N
ASP
80
A
O
VAL
493
A
O
VAL
85
A
N
LEU
419
A
N
LEU
11
A
O
SER
423
A
O
SER
15
A
N
LEU
426
A
N
LEU
18
A
O
LEU
458
A
O
LEU
50
A
N
ASP
464
A
N
ASP
56
A
O
MET
526
A
O
MET
118
A
N
LEU
525
A
N
LEU
117
A
O
PHE
514
A
O
PHE
106
A
N
HIS
517
A
N
HIS
109
A
O
ARG
505
A
O
ARG
97
1
A
CG
GLN
429
A
CG
GLN
21
1
Y
1
A
CD
GLN
429
A
CD
GLN
21
1
Y
1
A
OE1
GLN
429
A
OE1
GLN
21
1
Y
1
A
NE2
GLN
429
A
NE2
GLN
21
1
Y
1
A
CG
GLN
548
A
CG
GLN
140
1
Y
1
A
CD
GLN
548
A
CD
GLN
140
1
Y
1
A
OE1
GLN
548
A
OE1
GLN
140
1
Y
1
A
NE2
GLN
548
A
NE2
GLN
140
1
Y
1
A
CA
SER
549
A
CA
SER
141
1
Y
1
A
C
SER
549
A
C
SER
141
1
Y
1
A
O
SER
549
A
O
SER
141
1
Y
1
A
CB
SER
549
A
CB
SER
141
1
Y
1
A
OG
SER
549
A
OG
SER
141
1
Y
1
A
GLY
409
A
GLY
1
1
Y
1
A
HIS
550
A
HIS
142
1
Y
1
A
PRO
551
A
PRO
143
1
Y
1
A
ASP
552
A
ASP
144
1
Y
1
A
ALA
553
A
ALA
145
1
Y
1
A
ALA
554
A
ALA
146
1
Y
1
A
VAL
555
A
VAL
147
1
Y
1
A
GLN
556
A
GLN
148
1
Y
1
5.42
0.90
118.30
123.72
A
A
A
CB
CG
OD1
ASP
ASP
ASP
464
464
464
N
1
-3.60
0.50
120.30
116.70
A
A
A
NE
CZ
NH2
ARG
ARG
ARG
472
472
472
N
1
A
GLN
429
-99.73
52.95
1
A
GLU
480
-39.20
143.53
1
A
GLN
548
121.69
-70.98
21.05
0.12000
0.00000
0.00000
-0.64000
0.00000
0.52000
0.966
0.952
HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. DISORDERED RESIDUES WERE MODELLED AS ALA OR WITH OCCU 0.01. THE C-TERMINUS IS DISORDERED.
0.215
0.173
0.175
1.80
25.00
609
14309
4.100
99.5
2.765
0.084
RANDOM
LIKELY RESIDUAL
1
THROUGHOUT
MOLECULAR REPLACEMENT
0.121
0.120
0.80
0.80
1.40
PDB ENTRY 1W1D
MAXIMUM LIKELIHOOD
BABINET MODEL WITH MASK
1.80
25.00
112
1295
11
0
1172
0.016
0.021
1242
0.002
0.020
1101
1.681
1.944
1677
0.904
3.000
2566
7.298
5.000
138
0.106
0.200
170
0.010
0.020
1354
0.011
0.020
271
0.216
0.200
215
0.253
0.200
1257
0.086
0.200
730
0.160
0.200
89
0.190
0.200
17
0.312
0.200
79
0.117
0.200
12
0.983
1.500
700
1.780
2.000
1137
2.542
3.000
542
4.059
4.500
540
0.3480
0.2680
1.84
45
1000
20
1.80
25.00
2VKI
14950
2.0
0.06
1
10.00
4.5
100.0
0.55
1.80
1.86
2.30
1
4.3
100.0
refinement
REFMAC
5.1.24
data reduction
DENZO
data scaling
SCALEPACK
phasing
AMoRE
Structure of the PDK1 PH domain K465E mutant
1
N
N
2
N
N
3
N
N
4
N
N
A
ASN
411
A
ASN
3
HELX_P
A
GLN
414
A
GLN
6
5
1
4
A
SER
431
A
SER
23
HELX_P
A
ASN
446
A
ASN
38
1
2
16
A
TRP
448
A
TRP
40
HELX_P
A
VAL
452
A
VAL
44
5
3
5
A
ASN
531
A
ASN
123
HELX_P
A
GLN
548
A
GLN
140
1
4
18
TRANSFERASE
PLECKSTRIN HOMOLOGY, TRANSFERASE, CANCER, DIABETES
A
GLY
481
A
GLY
73
1
A
PRO
482
A
PRO
74
-4.30
PDPK1_HUMAN
UNP
1
O15530
409
556
2VKI
409
556
O15530
A
1
1
148
1
LYS
engineered mutation
GLU
465
2VKI
A
O15530
UNP
465
57
6
6
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
anti-parallel
A
ILE
416
A
ILE
8
A
ASP
420
A
ASP
12
A
SER
423
A
SER
15
A
LEU
426
A
LEU
18
A
ILE
457
A
ILE
49
A
GLU
465
A
GLU
57
A
ARG
472
A
ARG
64
A
THR
479
A
THR
71
A
HIS
483
A
HIS
75
A
ASP
488
A
ASP
80
A
VAL
493
A
VAL
85
A
ILE
498
A
ILE
90
A
ILE
416
A
ILE
8
A
ASP
420
A
ASP
12
A
SER
423
A
SER
15
A
LEU
426
A
LEU
18
A
ILE
457
A
ILE
49
A
GLU
465
A
GLU
57
A
ARG
521
A
ARG
113
A
MET
526
A
MET
118
A
THR
513
A
THR
105
A
THR
518
A
THR
110
A
ARG
505
A
ARG
97
A
ALA
508
A
ALA
100
BINDING SITE FOR RESIDUE GOL A1549
Software
4
BINDING SITE FOR RESIDUE SO4 A1550
Software
3
A
SER
431
A
SER
23
4
1_555
A
GLU
432
A
GLU
24
4
1_555
A
ASP
433
A
ASP
25
4
1_555
A
ARG
521
A
ARG
113
4
1_555
A
LYS
467
A
LYS
59
3
1_555
A
ARG
472
A
ARG
64
3
1_555
A
ARG
474
A
ARG
66
3
1_555
19
P 21 21 21