Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP0A9E5
DateThu Jan 5 11:10:00 GMT 2012
Unique Job IDcb46dee18dcbb2a1

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3d0sA_
Top template information
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein;
PDBTitle: camp receptor protein from m.tuberculosis, camp-free form
Confidence and coverage
Confidence:100.0% Coverage: 87%
218 residues ( 87% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MIPEKRIIRRIQSGGCAIHCQDCSISQLCIPFTLNEHELDQLDNIIERKKPIQKGQTLFK
Secondary structure 
SS confidence 
Disorder  ??????????????
???
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  AGDELKSLYAIRSGTIKSYTITEQGDEQITGFHLAGDLVGFDAIGSGHHPSFAQALETSM
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  VCEIPFETLDDLSGKMPNLRQQMMRLMSGEIKGDQDMILLLSKKNAEERLAAFIYNLSRR
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  FAQRGFSPREFRLTMTRGDIGNYLGLTVETISRLLGRFQKSGMLAVKGKYITIENNDALA
Secondary structure 
SS confidence 
Disorder  ?
???????
Disorder confidence 
 
   .........250
Sequence  QLAGHTRNVA
Secondary structure 
SS confidence 
Disorder 
???????
Disorder confidence 
 

Confidence Key
High(9)                    Low (0)
?Disordered
Alpha helix
Beta strand

Domain analysis 

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

RankAligned region

PDB 3d0s chain A

3D model

Region: 25 - 243
Aligned: 218
Modelled: 219
Confidence: 100.0%
Identity: 20%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein;
PDBTitle: camp receptor protein from m.tuberculosis, camp-free form

Phyre2

PDB 1zyb chain A

3D model

Region: 25 - 239
Aligned: 209
Modelled: 215
Confidence: 100.0%
Identity: 16%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcription regulator, crp family;
PDBTitle: crystal structure of transcription regulator from bacteroides2 thetaiotaomicron vpi-5482 at 2.15 a resolution

Phyre2

PDB 3dv8 chain A

3D model

Region: 28 - 243
Aligned: 208
Modelled: 216
Confidence: 100.0%
Identity: 20%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, crp/fnr family;
PDBTitle: crystal structure of a putative transcriptional regulator of the2 crp/fnr family (eubrec_1222) from eubacterium rectale atcc 33656 at3 2.55 a resolution

Phyre2

PDB 3fx3 chain A

3D model

Region: 25 - 245
Aligned: 210
Modelled: 221
Confidence: 100.0%
Identity: 21%
PDB header:camp-binding protein
Chain: A: PDB Molecule:cyclic nucleotide-binding protein;
PDBTitle: structure of a putative camp-binding regulatory protein from2 silicibacter pomeroyi dss-3

Phyre2

PDB 2bgc chain A

3D model

Region: 33 - 248
Aligned: 216
Modelled: 216
Confidence: 100.0%
Identity: 13%
PDB header:transcription
Chain: A: PDB Molecule:prfa;
PDBTitle: prfa-g145s, a constitutive active mutant of the2 transcriptional regulator in l.monocytogenes

Phyre2

PDB 2fmy chain B

3D model

Region: 23 - 244
Aligned: 214
Modelled: 215
Confidence: 100.0%
Identity: 20%
PDB header:dna binding protein
Chain: B: PDB Molecule:carbon monoxide oxidation system transcription regulator
PDBTitle: co-dependent transcription factor cooa from carboxydothermus2 hydrogenoformans (imidazole-bound form)

Phyre2

PDB 3e97 chain A

3D model

Region: 25 - 243
Aligned: 214
Modelled: 219
Confidence: 100.0%
Identity: 16%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, crp/fnr family;
PDBTitle: crystal structure of transcriptional regulator of crp/fnr2 family (yp_604437.1) from deinococcus geothermalis dsm3 11300 at 1.86 a resolution

Phyre2

PDB 3dkw chain B

3D model

Region: 25 - 242
Aligned: 214
Modelled: 215
Confidence: 100.0%
Identity: 20%
PDB header:transcription regulator
Chain: B: PDB Molecule:dnr protein;
PDBTitle: crystal structure of dnr from pseudomonas aeruginosa.

Phyre2

PDB 3e6d chain A

3D model

Region: 34 - 243
Aligned: 200
Modelled: 210
Confidence: 100.0%
Identity: 19%
PDB header:transcription regulation
Chain: A: PDB Molecule:cyclic nucleotide-binding protein;
PDBTitle: crystal structure of cprk c200s

Phyre2

PDB 2oz6 chain A

3D model

Region: 34 - 235
Aligned: 200
Modelled: 202
Confidence: 100.0%
Identity: 21%
PDB header:dna binding protein
Chain: A: PDB Molecule:virulence factor regulator;
PDBTitle: crystal structure of virulence factor regulator from pseudomonas2 aeruginosa in complex with camp

Phyre2

PDB 2zdb chain A

3D model

Region: 49 - 246
Aligned: 191
Modelled: 198
Confidence: 100.0%
Identity: 15%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, crp family;
PDBTitle: crystal structure of tthb099, a transcriptional regulator crp family2 from thermus thermophilus hb8

Phyre2

PDB 2gau chain A

3D model

Region: 30 - 244
Aligned: 209
Modelled: 215
Confidence: 100.0%
Identity: 25%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, crp/fnr family;
PDBTitle: crystal structure of transcriptional regulator, crp/fnr family from2 porphyromonas gingivalis (apc80792), structural genomics, mcsg

Phyre2

PDB 3la2 chain A

3D model

Region: 49 - 241
Aligned: 193
Modelled: 193
Confidence: 100.0%
Identity: 23%
PDB header:transcription
Chain: A: PDB Molecule:global nitrogen regulator;
PDBTitle: crystal structure of ntca in complex with 2-oxoglutarate

Phyre2

PDB 3iwz chain B

3D model

Region: 34 - 233
Aligned: 198
Modelled: 200
Confidence: 100.0%
Identity: 19%
PDB header:transcription
Chain: B: PDB Molecule:catabolite activation-like protein;
PDBTitle: the c-di-gmp responsive global regulator clp links cell-cell signaling2 to virulence gene expression in xanthomonas campestris

Phyre2

PDB 3kcc chain A

3D model

Region: 36 - 233
Aligned: 196
Modelled: 198
Confidence: 100.0%
Identity: 20%
PDB header:transcription
Chain: A: PDB Molecule:catabolite gene activator;
PDBTitle: crystal structure of d138l mutant of catabolite gene activator protein

Phyre2

PDB 1ft9 chain A

3D model

Region: 27 - 243
Aligned: 207
Modelled: 217
Confidence: 100.0%
Identity: 16%
PDB header:transcription
Chain: A: PDB Molecule:carbon monoxide oxidation system transcription
PDBTitle: structure of the reduced (feii) co-sensing protein from r.2 rubrum

Phyre2

PDB 2zcw chain A

3D model

Region: 50 - 246
Aligned: 189
Modelled: 197
Confidence: 99.9%
Identity: 16%
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, fnr/crp family;
PDBTitle: crystal structure of ttha1359, a transcriptional regulator,2 crp/fnr family from thermus thermophilus hb8

Phyre2

PDB 1zre chain B

3D model

Region: 36 - 233
Aligned: 196
Modelled: 198
Confidence: 99.9%
Identity: 21%
PDB header:gene regulation/dna
Chain: B: PDB Molecule:catabolite gene activator;
PDBTitle: 4 crystal structures of cap-dna with all base-pair2 substitutions at position 6, cap-[6g;17c]icap38 dna

Phyre2

PDB 1zyb chain A domain 2

3D model

Region: 25 - 160
Aligned: 136
Modelled: 136
Confidence: 99.7%
Identity: 14%
Fold: Double-stranded beta-helix
Superfamily: cAMP-binding domain-like
Family: cAMP-binding domain

Phyre2

PDB 3gyd chain A

3D model

Region: 25 - 165
Aligned: 140
Modelled: 141
Confidence: 99.7%
Identity: 12%
PDB header:dna binding protein
Chain: A: PDB Molecule:cyclic nucleotide-binding domain;
PDBTitle: crystal structure of a cyclic nucleotide-binding domain (mfla_1926)2 from methylobacillus flagellatus kt at 1.79 a resolution

Phyre2
1
c3d0sA_
2
c1zybA_
3
c3dv8A_
4
c3fx3A_
5
c2bgcA_
6
c2fmyB_
7
c3e97A_
8
c3dkwB_
9
c3e6dA_
10
c2oz6A_
11
c2zdbA_
12
c2gauA_
13
c3la2A_
14
c3iwzB_
15
c3kccA_
16
c1ft9A_
17
c2zcwA_
18
c1zreB_
19
d1zyba2
20
c3gydA_
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
244
245
246
247
248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
298
299
300
301
302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
318
319
320
321
322
323
324
325
326
327
328
329
330
331
332
333
334
335
336
337
338
339
340
341
342
343
344
345
346
347
348
349
350
351
352
353
354
355
356
357
358
359
360
361
362
363
364
365
366
367
368
369
370
371
372
373
374
375
376
377
378
379
380
381
382
383
384
385
386
387
388
389
390
391
392
393
394
395
396
397
398
399
400
401
402
403
404
405
406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
425
426
427
428
429
430
431
432
433
434
435
436
437
438
439
440
441
442
443
444
445
446
447
448
449
450
451
452
453
454
455
456
457
458
459
460
461
462
463
464
465
466
467
468
469
470
471
472
473
474
475
476
477
478
479
480
481
482
483
484
485
486
487
488
489
490
491
492
493
494
495
496
497
498
499



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3d0sA_
100.0 20 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein;
PDBTitle: camp receptor protein from m.tuberculosis, camp-free form
2c1zybA_
100.0 16 PDB header:transcription regulator
Chain: A: PDB Molecule:transcription regulator, crp family;
PDBTitle: crystal structure of transcription regulator from bacteroides2 thetaiotaomicron vpi-5482 at 2.15 a resolution
3c3dv8A_
100.0 20 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, crp/fnr family;
PDBTitle: crystal structure of a putative transcriptional regulator of the2 crp/fnr family (eubrec_1222) from eubacterium rectale atcc 33656 at3 2.55 a resolution
4c3fx3A_
100.0 21 PDB header:camp-binding protein
Chain: A: PDB Molecule:cyclic nucleotide-binding protein;
PDBTitle: structure of a putative camp-binding regulatory protein from2 silicibacter pomeroyi dss-3
5c2bgcA_
100.0 13 PDB header:transcription
Chain: A: PDB Molecule:prfa;
PDBTitle: prfa-g145s, a constitutive active mutant of the2 transcriptional regulator in l.monocytogenes
6c2fmyB_
100.0 20 PDB header:dna binding protein
Chain: B: PDB Molecule:carbon monoxide oxidation system transcription regulator
PDBTitle: co-dependent transcription factor cooa from carboxydothermus2 hydrogenoformans (imidazole-bound form)
7c3e97A_
100.0 16 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, crp/fnr family;
PDBTitle: crystal structure of transcriptional regulator of crp/fnr2 family (yp_604437.1) from deinococcus geothermalis dsm3 11300 at 1.86 a resolution
8c3dkwB_
100.0 20 PDB header:transcription regulator
Chain: B: PDB Molecule:dnr protein;
PDBTitle: crystal structure of dnr from pseudomonas aeruginosa.
9c3e6dA_
100.0 19 PDB header:transcription regulation
Chain: A: PDB Molecule:cyclic nucleotide-binding protein;
PDBTitle: crystal structure of cprk c200s
10c2oz6A_
100.0 21 PDB header:dna binding protein
Chain: A: PDB Molecule:virulence factor regulator;
PDBTitle: crystal structure of virulence factor regulator from pseudomonas2 aeruginosa in complex with camp
11c2zdbA_
100.0 15 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, crp family;
PDBTitle: crystal structure of tthb099, a transcriptional regulator crp family2 from thermus thermophilus hb8
12c2gauA_
100.0 25 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, crp/fnr family;
PDBTitle: crystal structure of transcriptional regulator, crp/fnr family from2 porphyromonas gingivalis (apc80792), structural genomics, mcsg
13c3la2A_
100.0 23 PDB header:transcription
Chain: A: PDB Molecule:global nitrogen regulator;
PDBTitle: crystal structure of ntca in complex with 2-oxoglutarate
14c3iwzB_
100.0 19 PDB header:transcription
Chain: B: PDB Molecule:catabolite activation-like protein;
PDBTitle: the c-di-gmp responsive global regulator clp links cell-cell signaling2 to virulence gene expression in xanthomonas campestris
15c3kccA_
100.0 20 PDB header:transcription
Chain: A: PDB Molecule:catabolite gene activator;
PDBTitle: crystal structure of d138l mutant of catabolite gene activator protein
16c1ft9A_
100.0 16 PDB header:transcription
Chain: A: PDB Molecule:carbon monoxide oxidation system transcription
PDBTitle: structure of the reduced (feii) co-sensing protein from r.2 rubrum
17c2zcwA_
99.9 16 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, fnr/crp family;
PDBTitle: crystal structure of ttha1359, a transcriptional regulator,2 crp/fnr family from thermus thermophilus hb8
18c1zreB_
99.9 21 PDB header:gene regulation/dna
Chain: B: PDB Molecule:catabolite gene activator;
PDBTitle: 4 crystal structures of cap-dna with all base-pair2 substitutions at position 6, cap-[6g;17c]icap38 dna
19d1zyba2
99.7 14 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
20c3gydA_
99.7 12 PDB header:dna binding protein
Chain: A: PDB Molecule:cyclic nucleotide-binding domain;
PDBTitle: crystal structure of a cyclic nucleotide-binding domain (mfla_1926)2 from methylobacillus flagellatus kt at 1.79 a resolution
21c2pqqD_
not modelled 99.7 17 PDB header:transcription
Chain: D: PDB Molecule:putative transcriptional regulator;
PDBTitle: structural genomics, the crystal structure of the n-terminal domain of2 a transcriptional regulator from streptomyces coelicolor a3(2)
22c3dn7A_
not modelled 99.6 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:cyclic nucleotide binding regulatory protein;
PDBTitle: cyclic nucleotide binding regulatory protein from cytophaga2 hutchinsonii.
23d3e5ua2
not modelled 99.6 15 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
24d2h6ca2
not modelled 99.5 16 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
25d2oz6a2
not modelled 99.5 20 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
26c3mdpA_
not modelled 99.5 17 PDB header:nucleotide binding protein
Chain: A: PDB Molecule:cyclic nucleotide-binding domain (cnmp-bd) protein;
PDBTitle: crystal structure of a putative cyclic nucleotide-binding protein2 (gmet_1532) from geobacter metallireducens gs-15 at 1.90 a resolution
27d1ft9a2
not modelled 99.5 15 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:CO-sensing protein CooA, N-terminal domain
28d1i5za2
not modelled 99.5 18 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
29c2z69A_
not modelled 99.5 17 PDB header:transcription regulator
Chain: A: PDB Molecule:dnr protein;
PDBTitle: crystal structure of the sensor domain of the transcriptional2 regulator dnr from pseudomonas aeruginosa
30d2gaua1
not modelled 99.5 27 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
31d2bgca1
not modelled 99.5 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
32d2gaua2
not modelled 99.5 26 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
33c1o5lA_
not modelled 99.5 20 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, crp family;
PDBTitle: crystal structure of transcriptional regulator (tm1171) from2 thermotoga maritima at 2.30 a resolution
34d1o5la1
not modelled 99.5 20 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
35d2h6ca1
not modelled 99.5 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
36d2coha2
not modelled 99.5 15 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
37d1cx4a2
not modelled 99.5 13 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
38d1ne6a2
not modelled 99.4 13 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
39d1wgpa_
not modelled 99.4 15 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
40d1cx4a1
not modelled 99.4 14 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
41c1o7fA_
not modelled 99.4 18 PDB header:regulation
Chain: A: PDB Molecule:camp-dependent rap1 guanine-nucleotide exchange
PDBTitle: crystal structure of the regulatory domain of epac2
42d2coha1
not modelled 99.4 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
43c2byvE_
not modelled 99.4 18 PDB header:regulation
Chain: E: PDB Molecule:rap guanine nucleotide exchange factor 4;
PDBTitle: structure of the camp responsive exchange factor epac2 in2 its auto-inhibited state
44d1o7fa2
not modelled 99.4 17 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
45d3e5ua1
not modelled 99.4 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
46c3idcB_
not modelled 99.3 13 PDB header:transferase
Chain: B: PDB Molecule:camp-dependent protein kinase type ii-beta
PDBTitle: crystal structure of (102-265)riib:c holoenzyme of camp-2 dependent protein kinase
47d1ft9a1
not modelled 99.3 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
48d1vp6a_
not modelled 99.3 12 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
49d1ne6a1
not modelled 99.3 16 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
50c3ogjD_
not modelled 99.3 13 PDB header:transferase
Chain: D: PDB Molecule:prkg1 protein;
PDBTitle: crystal structure of partial apo (92-227) of cgmp-dependent protein2 kinase
51c3pvbB_
not modelled 99.2 16 PDB header:transferase
Chain: B: PDB Molecule:camp-dependent protein kinase type i-alpha regulatory
PDBTitle: crystal structure of (73-244)ria:c holoenzyme of camp-dependent2 protein kinase
52d2oz6a1
not modelled 99.2 24 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
53c1cx4A_
not modelled 99.2 13 PDB header:signaling protein
Chain: A: PDB Molecule:camp-dependent protein kinase regulatory subunit
PDBTitle: crystal structure of a deletion mutant of the type ii beta2 regulatory subunit of camp-dependent protein kinase
54d1i5za1
not modelled 99.1 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
55d1o7fa3
not modelled 99.1 16 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
56c3otfA_
not modelled 99.1 12 PDB header:transport protein
Chain: A: PDB Molecule:potassium/sodium hyperpolarization-activated cyclic
PDBTitle: structural basis for the camp-dependent gating in human hcn4 channel
57c2ptmA_
not modelled 99.1 10 PDB header:transport protein
Chain: A: PDB Molecule:hyperpolarization-activated (ih) channel;
PDBTitle: structure and rearrangements in the carboxy-terminal region of spih2 channels
58d1q3ea_
not modelled 99.1 11 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:cAMP-binding domain
59c3uknC_
not modelled 99.0 22 PDB header:transport protein, membrane protein
Chain: C: PDB Molecule:novel protein similar to vertebrate potassium voltage-gated
PDBTitle: structure of the c-linker/cnbhd of zelk channels in c 2 2 21 space2 group
60c3cf6E_
not modelled 99.0 17 PDB header:signaling protein/gtp-binding protein
Chain: E: PDB Molecule:rap guanine nucleotide exchange factor (gef) 4;
PDBTitle: structure of epac2 in complex with cyclic-amp and rap
61c1rgsA_
not modelled 99.0 15 PDB header:kinase
Chain: A: PDB Molecule:camp dependent protein kinase;
PDBTitle: regulatory subunit of camp dependent protein kinase
62c3shrA_
not modelled 99.0 12 PDB header:transferase
Chain: A: PDB Molecule:cgmp-dependent protein kinase 1;
PDBTitle: crystal structure of cgmp-dependent protein kinase reveals novel site2 of interchain communication
63c2d93A_
not modelled 98.9 15 PDB header:signaling protein
Chain: A: PDB Molecule:rap guanine nucleotide exchange factor 6;
PDBTitle: solution structure of the cnmp_binding domain of human rap2 guanine nucleotide exchange factor 6
64c3of1A_
not modelled 98.9 17 PDB header:transferase
Chain: A: PDB Molecule:camp-dependent protein kinase regulatory subunit;
PDBTitle: crystal structure of bcy1, the yeast regulatory subunit of pka
65d1zyba1
not modelled 97.9 22 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:CAP C-terminal domain-like
66d2bgca2
not modelled 97.6 14 Fold:Double-stranded beta-helix
Superfamily:cAMP-binding domain-like
Family:Listeriolysin regulatory protein PrfA, N-terminal domain
67c2x4hA_
not modelled 97.3 14 PDB header:transcription
Chain: A: PDB Molecule:hypothetical protein sso2273;
PDBTitle: crystal structure of the hypothetical protein sso2273 from2 sulfolobus solfataricus
68c2w48D_
not modelled 97.2 29 PDB header:transcription
Chain: D: PDB Molecule:sorbitol operon regulator;
PDBTitle: crystal structure of the full-length sorbitol operon2 regulator sorc from klebsiella pneumoniae
69c2h09A_
not modelled 97.0 14 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator mntr;
PDBTitle: crystal structure of diphtheria toxin repressor like protein2 from e. coli
70c2it0A_
not modelled 97.0 17 PDB header:transcription/dna
Chain: A: PDB Molecule:iron-dependent repressor ider;
PDBTitle: crystal structure of a two-domain ider-dna complex crystal2 form ii
71c1f5tA_
not modelled 97.0 14 PDB header:transcription/dna
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: diphtheria tox repressor (c102d mutant) complexed with2 nickel and dtxr consensus binding sequence
72d2fxaa1
not modelled 96.9 13 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
73d2d1ha1
not modelled 96.8 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
74d1g3wa1
not modelled 96.8 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
75d3ctaa1
not modelled 96.7 20 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
76d2isya1
not modelled 96.7 30 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
77d1z05a1
not modelled 96.7 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ROK associated domain
78d1hw1a1
not modelled 96.7 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
79c1fx7C_
not modelled 96.7 14 PDB header:signaling protein
Chain: C: PDB Molecule:iron-dependent repressor ider;
PDBTitle: crystal structure of the iron-dependent regulator (ider)2 from mycobacterium tuberculosis
80c3bj6B_
not modelled 96.7 14 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of marr family transcription regulator sp03579
81c1g3wA_
not modelled 96.7 19 PDB header:gene regulation
Chain: A: PDB Molecule:diphtheria toxin repressor;
PDBTitle: cd-cys102ser dtxr
82c3eetA_
not modelled 96.6 14 PDB header:transcription regulator
Chain: A: PDB Molecule:putative gntr-family transcriptional regulator;
PDBTitle: crystal structure of putative gntr-family transcriptional2 regulator
83c2fxaB_
not modelled 96.6 14 PDB header:transcription
Chain: B: PDB Molecule:protease production regulatory protein hpr;
PDBTitle: structure of the protease production regulatory protein hpr from2 bacillus subtilis.
84c3g3zA_
not modelled 96.5 12 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the structure of nmb1585, a marr family regulator from neisseria2 meningitidis
85c2qwwB_
not modelled 96.5 8 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: crystal structure of multiple antibiotic-resistance repressor (marr)2 (yp_013417.1) from listeria monocytogenes 4b f2365 at 2.07 a3 resolution
86c3ctaA_
not modelled 96.5 20 PDB header:transferase
Chain: A: PDB Molecule:riboflavin kinase;
PDBTitle: crystal structure of riboflavin kinase from thermoplasma2 acidophilum
87c2rdpA_
not modelled 96.5 12 PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator marr;
PDBTitle: the structure of a marr family protein from bacillus2 stearothermophilus
88d3broa1
not modelled 96.5 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
89c2pexA_
not modelled 96.5 20 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator ohrr;
PDBTitle: structure of reduced c22s ohrr from xanthamonas campestris
90c3nqoB_
not modelled 96.5 15 PDB header:transcription
Chain: B: PDB Molecule:marr-family transcriptional regulator;
PDBTitle: crystal structure of a marr family transcriptional regulator (cd1569)2 from clostridium difficile 630 at 2.20 a resolution
91d2ev0a1
not modelled 96.5 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Iron-dependent repressor protein
92d1ku9a_
not modelled 96.4 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:DNA-binding protein Mj223
93c3hruA_
not modelled 96.4 8 PDB header:transcription
Chain: A: PDB Molecule:metalloregulator scar;
PDBTitle: crystal structure of scar with bound zn2+
94d2hr3a1
not modelled 96.4 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
95d1lnwa_
not modelled 96.4 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
96c3s2wB_
not modelled 96.3 10 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, marr family;
PDBTitle: the crystal structure of a marr transcriptional regulator from2 methanosarcina mazei go1
97d2etha1
not modelled 96.3 9 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
98d1s3ja_
not modelled 96.3 11 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
99c3edpB_
not modelled 96.3 14 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:lin2111 protein;
PDBTitle: the crystal structure of the protein lin2111 (functionally unknown)2 from listeria innocua clip11262
100c2du9A_
not modelled 96.3 12 PDB header:transcription
Chain: A: PDB Molecule:predicted transcriptional regulators;
PDBTitle: crystal structure of the transcriptional factor from c.glutamicum
101c2nyxB_
not modelled 96.3 11 PDB header:transcription
Chain: B: PDB Molecule:probable transcriptional regulatory protein, rv1404;
PDBTitle: crystal structure of rv1404 from mycobacterium tuberculosis
102c2ev5B_
not modelled 96.3 15 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator mntr;
PDBTitle: bacillus subtilis manganese transport regulator (mntr)2 bound to calcium
103c3neuA_
not modelled 96.2 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin1836 protein;
PDBTitle: the crystal structure of a functionally-unknown protein lin1836 from2 listeria innocua clip11262
104d1sfxa_
not modelled 96.2 18 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:TrmB-like
105d3deua1
not modelled 96.2 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
106c2fa5B_
not modelled 96.2 9 PDB header:transcription
Chain: B: PDB Molecule:transcriptional regulator marr/emrr family;
PDBTitle: the crystal structure of an unliganded multiple antibiotic-2 resistance repressor (marr) from xanthomonas campestris
107d1z6ra1
not modelled 96.2 14 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:ROK associated domain
108c3r0aB_
not modelled 96.2 18 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: possible transcriptional regulator from methanosarcina mazei go1 (gi2 21227196)
109c3f8mA_
not modelled 96.1 16 PDB header:transcription
Chain: A: PDB Molecule:gntr-family protein transcriptional regulator;
PDBTitle: crystal structure of phnf from mycobacterium smegmatis
110c3tgnA_
not modelled 96.1 18 PDB header:transcription
Chain: A: PDB Molecule:adc operon repressor adcr;
PDBTitle: crystal structure of the zinc-dependent marr family transcriptional2 regulator adcr in the zn(ii)-bound state
111c2hoeA_
not modelled 96.1 25 PDB header:transferase
Chain: A: PDB Molecule:n-acetylglucosamine kinase;
PDBTitle: crystal structure of n-acetylglucosamine kinase (tm1224) from2 thermotoga maritima at 2.46 a resolution
112d2fbha1
not modelled 96.0 19 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
113c3bddD_
not modelled 96.0 17 PDB header:transcription
Chain: D: PDB Molecule:regulatory protein marr;
PDBTitle: crystal structure of a putative multiple antibiotic-resistance2 repressor (ssu05_1136) from streptococcus suis 89/1591 at 2.20 a3 resolution
114d2hs5a1
not modelled 96.0 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:GntR-like transcriptional regulators
115c3deuB_
not modelled 96.0 12 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator slya;
PDBTitle: crystal structure of transcription regulatory protein slya2 from salmonella typhimurium in complex with salicylate3 ligands
116c3nrvC_
not modelled 96.0 22 PDB header:transcription regulator
Chain: C: PDB Molecule:putative transcriptional regulator (marr/emrr family);
PDBTitle: crystal structure of marr/emrr family transcriptional regulator from2 acinetobacter sp. adp1
117c3by6C_
not modelled 96.0 13 PDB header:transcription regulator
Chain: C: PDB Molecule:predicted transcriptional regulator;
PDBTitle: crystal structure of a transcriptional regulator from oenococcus oeni
118d2frha1
not modelled 96.0 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:MarR-like transcriptional regulators
119d1j5ya1
not modelled 96.0 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Biotin repressor-like
120c2hs5A_
not modelled 95.9 15 PDB header:transcription regulator
Chain: A: PDB Molecule:putative transcriptional regulator gntr;
PDBTitle: structural genomics, the crystal structure of a putative2 transcriptional regulator gntr from rhodococcus sp. rha1

Binding site prediction 

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite


Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
 
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
 
© Structural Bioinformatics Group
Imperial College London
Lawrence Kelley, Benjamin Jefferys
Disclaimer
Terms and Conditions
Component software
Template detection: HHpred 1.51
Secondary structure prediction: Psi-pred 2.5
Disorder prediction: Disopred 2.4
Transmembrane prediction: Memsat_SVM
Multi-template modelling and ab initio: Poing 1.0