Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP77402
DateThu Jan 5 12:28:57 GMT 2012
Unique Job IDae53aed35555a1f3

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3gbgA_
Top template information
PDB header:transcription regulator
Chain: A: PDB Molecule:tcp pilus virulence regulatory protein;
PDBTitle: crystal structure of toxt from vibrio cholerae o395
Confidence and coverage
Confidence:100.0% Coverage: 83%
253 residues ( 83% 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  MYQRCFDNASETLFVAGKTPRLSRFAFSDDPKWESGHHVHDNETELIYVKKGVARFTIDS
Secondary structure 
SS confidence 
Disorder  ??????
?
??
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  SLYVAHADDIVVIERGRLHAVASDVNDPATTCTCALYGFQFQGAEENQLLQPHSCPVIAA
Secondary structure 
SS confidence 
Disorder 
?
???
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  GQGKEVIKTLFNELSVILPQSKNSQTSSLWDAFAYTLAILYYENFKNAYRSEQGYIKKDV
Secondary structure 
SS confidence 
Disorder 
??
?????
??????????????
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  LIKDILFYLNNNYREKITLEQLSKKFRASVSYICHEFTKEYRISPINYVIQRRMTEAKWS
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  LTNTELSQAEISWRVGYENVDHFAKLFLRHVGCSPSDYRRQFKNCFAEQEILSEFPQPVS
Secondary structure 
SS confidence 
Disorder 
??
????????????
????
Disorder confidence 
 
   ...
Sequence  LVG
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 3gbg chain A

3D model

Region: 21 - 284
Aligned: 253
Modelled: 264
Confidence: 100.0%
Identity: 8%
PDB header:transcription regulator
Chain: A: PDB Molecule:tcp pilus virulence regulatory protein;
PDBTitle: crystal structure of toxt from vibrio cholerae o395

Phyre2

PDB 3oou chain A

3D model

Region: 181 - 283
Aligned: 103
Modelled: 103
Confidence: 99.9%
Identity: 26%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin2118 protein;
PDBTitle: the structure of a protein with unkown function from listeria innocua

Phyre2

PDB 1d5y chain D

3D model

Region: 178 - 281
Aligned: 104
Modelled: 104
Confidence: 99.9%
Identity: 19%
PDB header:transcription/dna
Chain: D: PDB Molecule:rob transcription factor;
PDBTitle: crystal structure of the e. coli rob transcription factor2 in complex with dna

Phyre2

PDB 3oio chain A

3D model

Region: 175 - 284
Aligned: 110
Modelled: 110
Confidence: 99.9%
Identity: 17%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (arac-type dna-binding domain-
PDBTitle: crystal structure of transcriptional regulator (arac-type dna-binding2 domain-containing proteins) from chromobacterium violaceum

Phyre2

PDB 3mn2 chain B

3D model

Region: 180 - 283
Aligned: 104
Modelled: 104
Confidence: 99.9%
Identity: 22%
PDB header:transcription regulator
Chain: B: PDB Molecule:probable arac family transcriptional regulator;
PDBTitle: the crystal structure of a probable arac family transcriptional2 regulator from rhodopseudomonas palustris cga009

Phyre2

PDB 1bl0 chain A

3D model

Region: 178 - 284
Aligned: 107
Modelled: 107
Confidence: 99.9%
Identity: 23%
PDB header:transcription/dna
Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein);
PDBTitle: multiple antibiotic resistance protein (mara)/dna complex

Phyre2

PDB 2k9s chain A

3D model

Region: 179 - 281
Aligned: 103
Modelled: 103
Confidence: 99.9%
Identity: 22%
PDB header:transcription
Chain: A: PDB Molecule:arabinose operon regulatory protein;
PDBTitle: solution structure of dna binding domain of e. coli arac

Phyre2

PDB 3mkl chain B

3D model

Region: 175 - 285
Aligned: 110
Modelled: 111
Confidence: 99.9%
Identity: 18%
PDB header:transcription regulator
Chain: B: PDB Molecule:hth-type transcriptional regulator gadx;
PDBTitle: crystal structure of dna-binding transcriptional dual regulator from2 escherichia coli k-12

Phyre2

PDB 3lsg chain D

3D model

Region: 183 - 271
Aligned: 89
Modelled: 89
Confidence: 99.8%
Identity: 33%
PDB header:transcription regulator
Chain: D: PDB Molecule:two-component response regulator yesn;
PDBTitle: the crystal structure of the c-terminal domain of the two-2 component response regulator yesn from fusobacterium3 nucleatum subsp. nucleatum atcc 25586

Phyre2

PDB 1d5y chain A domain 2

3D model

Region: 233 - 296
Aligned: 64
Modelled: 64
Confidence: 99.4%
Identity: 16%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2

PDB 1bl0 chain A domain 2

3D model

Region: 233 - 280
Aligned: 48
Modelled: 48
Confidence: 99.4%
Identity: 23%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2

PDB 2arc chain A

3D model

Region: 30 - 162
Aligned: 132
Modelled: 133
Confidence: 98.8%
Identity: 8%
Fold: Double-stranded beta-helix
Superfamily: Regulatory protein AraC
Family: Regulatory protein AraC

Phyre2

PDB 1d5y chain A domain 1

3D model

Region: 178 - 230
Aligned: 53
Modelled: 53
Confidence: 98.8%
Identity: 17%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2

PDB 1bl0 chain A domain 1

3D model

Region: 178 - 230
Aligned: 53
Modelled: 53
Confidence: 98.8%
Identity: 25%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: Homeodomain-like
Family: AraC type transcriptional activator

Phyre2

PDB 1zgw chain A

3D model

Region: 178 - 236
Aligned: 57
Modelled: 59
Confidence: 98.6%
Identity: 18%
PDB header:transcription regulator/dna
Chain: A: PDB Molecule:ada polyprotein;
PDBTitle: nmr structure of e. coli ada protein in complex with dna

Phyre2

PDB 3ibm chain B

3D model

Region: 19 - 98
Aligned: 79
Modelled: 80
Confidence: 98.4%
Identity: 18%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:cupin 2, conserved barrel domain protein;
PDBTitle: crystal structure of cupin 2 domain-containing protein hhal_0468 from2 halorhodospira halophila

Phyre2

PDB 3kgz chain A

3D model

Region: 13 - 108
Aligned: 95
Modelled: 96
Confidence: 98.4%
Identity: 13%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:cupin 2 conserved barrel domain protein;
PDBTitle: crystal structure of a cupin 2 conserved barrel domain protein from2 rhodopseudomonas palustris

Phyre2

PDB 3jzv chain A

3D model

Region: 5 - 95
Aligned: 90
Modelled: 89
Confidence: 98.4%
Identity: 13%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein rru_a2000;
PDBTitle: crystal structure of rru_a2000 from rhodospirillum rubrum: a cupin-22 domain.

Phyre2

PDB 1o4t chain A

3D model

Region: 18 - 97
Aligned: 80
Modelled: 80
Confidence: 98.3%
Identity: 18%
Fold: Double-stranded beta-helix
Superfamily: RmlC-like cupins
Family: TM1287-like

Phyre2

PDB 3cew chain A

3D model

Region: 20 - 108
Aligned: 89
Modelled: 86
Confidence: 98.3%
Identity: 13%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized cupin protein;
PDBTitle: crystal structure of a cupin protein (bf4112) from bacteroides2 fragilis. northeast structural genomics consortium target bfr205

Phyre2
1
c3gbgA_
2
c3oouA_
3
c1d5yD_
4
c3oioA_
5
c3mn2B_
6
c1bl0A_
7
c2k9sA_
8
c3mklB_
9
c3lsgD_
10
d1d5ya2
11
d1bl0a2
12
d2arca_
13
d1d5ya1
14
d1bl0a1
15
c1zgwA_
16
c3ibmB_
17
c3kgzA_
18
c3jzvA_
19
d1o4ta_
20
c3cewA_
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
1c3gbgA_
100.0 8 PDB header:transcription regulator
Chain: A: PDB Molecule:tcp pilus virulence regulatory protein;
PDBTitle: crystal structure of toxt from vibrio cholerae o395
2c3oouA_
99.9 26 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:lin2118 protein;
PDBTitle: the structure of a protein with unkown function from listeria innocua
3c1d5yD_
99.9 19 PDB header:transcription/dna
Chain: D: PDB Molecule:rob transcription factor;
PDBTitle: crystal structure of the e. coli rob transcription factor2 in complex with dna
4c3oioA_
99.9 17 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (arac-type dna-binding domain-
PDBTitle: crystal structure of transcriptional regulator (arac-type dna-binding2 domain-containing proteins) from chromobacterium violaceum
5c3mn2B_
99.9 22 PDB header:transcription regulator
Chain: B: PDB Molecule:probable arac family transcriptional regulator;
PDBTitle: the crystal structure of a probable arac family transcriptional2 regulator from rhodopseudomonas palustris cga009
6c1bl0A_
99.9 23 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (multiple antibiotic resistance protein);
PDBTitle: multiple antibiotic resistance protein (mara)/dna complex
7c2k9sA_
99.9 22 PDB header:transcription
Chain: A: PDB Molecule:arabinose operon regulatory protein;
PDBTitle: solution structure of dna binding domain of e. coli arac
8c3mklB_
99.9 18 PDB header:transcription regulator
Chain: B: PDB Molecule:hth-type transcriptional regulator gadx;
PDBTitle: crystal structure of dna-binding transcriptional dual regulator from2 escherichia coli k-12
9c3lsgD_
99.8 33 PDB header:transcription regulator
Chain: D: PDB Molecule:two-component response regulator yesn;
PDBTitle: the crystal structure of the c-terminal domain of the two-2 component response regulator yesn from fusobacterium3 nucleatum subsp. nucleatum atcc 25586
10d1d5ya2
99.4 16 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
11d1bl0a2
99.4 23 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
12d2arca_
98.8 8 Fold:Double-stranded beta-helix
Superfamily:Regulatory protein AraC
Family:Regulatory protein AraC
13d1d5ya1
98.8 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
14d1bl0a1
98.8 25 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:AraC type transcriptional activator
15c1zgwA_
98.6 18 PDB header:transcription regulator/dna
Chain: A: PDB Molecule:ada polyprotein;
PDBTitle: nmr structure of e. coli ada protein in complex with dna
16c3ibmB_
98.4 18 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:cupin 2, conserved barrel domain protein;
PDBTitle: crystal structure of cupin 2 domain-containing protein hhal_0468 from2 halorhodospira halophila
17c3kgzA_
98.4 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:cupin 2 conserved barrel domain protein;
PDBTitle: crystal structure of a cupin 2 conserved barrel domain protein from2 rhodopseudomonas palustris
18c3jzvA_
98.4 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein rru_a2000;
PDBTitle: crystal structure of rru_a2000 from rhodospirillum rubrum: a cupin-22 domain.
19d1o4ta_
98.3 18 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1287-like
20c3cewA_
98.3 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized cupin protein;
PDBTitle: crystal structure of a cupin protein (bf4112) from bacteroides2 fragilis. northeast structural genomics consortium target bfr205
21d1y3ta1
not modelled 98.3 13 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Quercetin 2,3-dioxygenase-like
22d1v70a_
not modelled 98.3 13 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1287-like
23d1vj2a_
not modelled 98.3 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1459-like
24c2gu9B_
not modelled 98.3 18 PDB header:immune system
Chain: B: PDB Molecule:tetracenomycin polyketide synthesis protein;
PDBTitle: crystal structure of xc5357 from xanthomonas campestris: a2 putative tetracenomycin polyketide synthesis protein3 adopting a novel cupin subfamily structure
25c3h7yA_
not modelled 98.2 10 PDB header:biosynthetic protein
Chain: A: PDB Molecule:bacilysin biosynthesis protein bacb;
PDBTitle: crystal structure of bacb, an enzyme involved in bacilysin synthesis,2 in tetragonal form
26c2vpvA_
not modelled 98.2 11 PDB header:cell cycle
Chain: A: PDB Molecule:protein mif2;
PDBTitle: dimerization domain of mif2p
27d1y9qa2
not modelled 98.2 17 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Probable transcriptional regulator VC1968, C-terminal domain
28d1sfna_
not modelled 98.1 10 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:YlbA-like
29c3h8uA_
not modelled 98.1 19 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized conserved protein with double-stranded
PDBTitle: crystal structure of uncharacterized conserved protein with double-2 stranded beta-helix domain (yp_001338853.1) from klebsiella3 pneumoniae subsp. pneumoniae mgh 78578 at 1.80 a resolution
30c3i7dB_
not modelled 98.1 18 PDB header:isomerase
Chain: B: PDB Molecule:sugar phosphate isomerase;
PDBTitle: crystal structure of sugar phosphate isomerase from a cupin2 superfamily spo2919 from silicibacter pomeroyi (yp_168127.1) from3 silicibacter pomeroyi dss-3 at 2.30 a resolution
31c3l2hD_
not modelled 98.1 20 PDB header:isomerase
Chain: D: PDB Molecule:putative sugar phosphate isomerase;
PDBTitle: crystal structure of putative sugar phosphate isomerase (afe_0303)2 from acidithiobacillus ferrooxidans atcc 23270 at 1.85 a resolution
32c2oa2A_
not modelled 98.1 18 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:bh2720 protein;
PDBTitle: crystal structure of bh2720 (10175341) from bacillus halodurans at2 1.41 a resolution
33c1sefA_
not modelled 98.1 10 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:conserved hypothetical protein;
PDBTitle: crystal structure of cupin domain protein ef2996 from enterococcus2 faecalis
34d1sefa_
not modelled 98.1 10 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:YlbA-like
35c3d82A_
not modelled 98.1 19 PDB header:metal binding protein
Chain: A: PDB Molecule:cupin 2, conserved barrel domain protein;
PDBTitle: crystal structure of a cupin-2 domain containing protein (sfri_3543)2 from shewanella frigidimarina ncimb 400 at 2.05 a resolution
36d3bu7a1
not modelled 98.1 12 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Gentisate 1,2-dioxygenase-like
37c3bu7A_
not modelled 98.1 12 PDB header:oxidoreductase
Chain: A: PDB Molecule:gentisate 1,2-dioxygenase;
PDBTitle: crystal structure and biochemical characterization of gdosp,2 a gentisate 1,2-dioxygenase from silicibacter pomeroyi
38c2ozjB_
not modelled 98.1 14 PDB header:unknown function
Chain: B: PDB Molecule:cupin 2, conserved barrel;
PDBTitle: crystal structure of a cupin superfamily protein (dsy2733) from2 desulfitobacterium hafniense dcb-2 at 1.60 a resolution
39d2f4pa1
not modelled 98.0 11 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1287-like
40c3fjsC_
not modelled 98.0 18 PDB header:biosynthetic protein
Chain: C: PDB Molecule:uncharacterized protein with rmlc-like cupin fold;
PDBTitle: crystal structure of a putative biosynthetic protein with rmlc-like2 cupin fold (reut_b4087) from ralstonia eutropha jmp134 at 1.90 a3 resolution
41d1sq4a_
not modelled 98.0 11 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:YlbA-like
42c2fqpD_
not modelled 98.0 15 PDB header:metal binding protein
Chain: D: PDB Molecule:hypothetical protein bp2299;
PDBTitle: crystal structure of a cupin domain (bp2299) from bordetella pertussis2 tohama i at 1.80 a resolution
43c3rnsA_
not modelled 98.0 13 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:cupin 2 conserved barrel domain protein;
PDBTitle: cupin 2 conserved barrel domain protein from leptotrichia buccalis
44c2i45C_
not modelled 98.0 13 PDB header:structural genomics, unknown function
Chain: C: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of protein nmb1881 from neisseria meningitidis
45d2phda1
not modelled 98.0 9 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Gentisate 1,2-dioxygenase-like
46d1uika1
not modelled 98.0 20 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
47d1yhfa1
not modelled 98.0 19 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1287-like
48d1lr5a_
not modelled 98.0 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
49c2d40C_
not modelled 98.0 14 PDB header:oxidoreductase
Chain: C: PDB Molecule:putative gentisate 1,2-dioxygenase;
PDBTitle: crystal structure of z3393 from escherichia coli o157:h7
50d2d40a1
not modelled 98.0 14 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Gentisate 1,2-dioxygenase-like
51d1juha_
not modelled 97.9 17 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Quercetin 2,3-dioxygenase-like
52c2o8qA_
not modelled 97.9 19 PDB header:metal binding protein
Chain: A: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of a protein with a cupin-like fold and unknown2 function (bxe_c0505) from burkholderia xenovorans lb400 at 1.55 a3 resolution
53c2pfwB_
not modelled 97.9 18 PDB header:unknown function
Chain: B: PDB Molecule:cupin 2, conserved barrel domain protein;
PDBTitle: crystal structure of a rmlc-like cupin (sfri_3105) from shewanella2 frigidimarina ncimb 400 at 1.90 a resolution
54c2vqaC_
not modelled 97.9 22 PDB header:metal-binding protein
Chain: C: PDB Molecule:sll1358 protein;
PDBTitle: protein-folding location can regulate mn versus cu- or zn-2 binding. crystal structure of mnca.
55c3ht2A_
not modelled 97.9 17 PDB header:lyase
Chain: A: PDB Molecule:remf protein;
PDBTitle: zink containing polyketide cyclase remf from streptomyces2 resistomycificus
56d2b8ma1
not modelled 97.9 12 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:MJ0764-like
57d1uija1
not modelled 97.9 21 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
58c2q30C_
not modelled 97.8 15 PDB header:unknown function
Chain: C: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a rmlc-like cupin protein (dde_2303) from2 desulfovibrio desulfuricans subsp. at 1.94 a resolution
59d2et1a1
not modelled 97.8 27 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
60c2oziA_
not modelled 97.8 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein rpa4178;
PDBTitle: structural genomics, the crystal structure of a putative2 protein rpa4178 from rhodopseudomonas palustris cga009
61d1j58a_
not modelled 97.8 19 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
62d1dgwa_
not modelled 97.8 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
63d1yfua1
not modelled 97.8 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:3-hydroxyanthranilic acid dioxygenase-like
64d1rc6a_
not modelled 97.7 9 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:YlbA-like
65c3lwcA_
not modelled 97.7 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of structural genomics, unknown function2 (yp_766765.1) from rhizobium leguminosarum bv. viciae 3841 at 1.40 a3 resolution
66d2phla2
not modelled 97.5 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
67d1x82a_
not modelled 97.5 11 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Glucose-6-phosphate isomerase, GPI
68d1j3pa_
not modelled 97.5 12 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Glucose-6-phosphate isomerase, GPI
69d2bnma2
not modelled 97.4 13 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:TM1459-like
70d1uija2
not modelled 97.4 15 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
71c1cauB_
not modelled 97.4 14 PDB header:seed storage protein
Chain: B: PDB Molecule:canavalin;
PDBTitle: determination of three crystal structures of canavalin by molecular2 replacement
72d1zvfa1
not modelled 97.4 15 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:3-hydroxyanthranilic acid dioxygenase-like
73d1zrra1
not modelled 97.4 11 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Acireductone dioxygenase
74d1uika2
not modelled 97.4 14 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
75d1od5a2
not modelled 97.4 15 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
76c2cauA_
not modelled 97.2 12 PDB header:plant protein
Chain: A: PDB Molecule:protein (canavalin);
PDBTitle: canavalin from jack bean
77d1fxza1
not modelled 97.2 14 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
78c3kglB_
not modelled 97.1 15 PDB header:plant protein
Chain: B: PDB Molecule:cruciferin;
PDBTitle: crystal structure of procruciferin, 11s globulin from2 brassica napus
79d1fxza2
not modelled 97.1 16 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
80c3kscD_
not modelled 97.1 20 PDB header:plant protein
Chain: D: PDB Molecule:lega class;
PDBTitle: crystal structure of pea prolegumin, an 11s seed globulin2 from pisum sativum l.
81c1y9qA_
not modelled 97.1 15 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, hth_3 family;
PDBTitle: crystal structure of hth_3 family transcriptional regulator2 from vibrio cholerae
82c2e9qA_
not modelled 97.1 15 PDB header:plant protein
Chain: A: PDB Molecule:11s globulin subunit beta;
PDBTitle: recombinant pro-11s globulin of pumpkin
83c2xlfA_
not modelled 97.0 11 PDB header:metal binding protein
Chain: A: PDB Molecule:sll1785 protein;
PDBTitle: structure and metal-loading of a soluble periplasm cupro-protein:2 apo-cuca-closed (semet)
84c1fxzC_
not modelled 97.0 18 PDB header:plant protein
Chain: C: PDB Molecule:glycinin g1;
PDBTitle: crystal structure of soybean proglycinin a1ab1b homotrimer
85c3es1A_
not modelled 97.0 22 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:cupin 2, conserved barrel domain protein;
PDBTitle: crystal structure of protein with a cupin-like fold and unknown2 function (yp_001165807.1) from novosphingobium aromaticivorans dsm3 12444 at 1.91 a resolution
86c3bcwB_
not modelled 96.9 16 PDB header:unknown function
Chain: B: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a duf861 family protein with a rmlc-like cupin2 fold (bb1179) from bordetella bronchiseptica rb50 at 1.60 a3 resolution
87c2eaaB_
not modelled 96.9 14 PDB header:plant protein
Chain: B: PDB Molecule:7s globulin-3;
PDBTitle: crystal structure of adzuki bean 7s globulin-3
88c2opkC_
not modelled 96.9 13 PDB header:isomerase
Chain: C: PDB Molecule:hypothetical protein;
PDBTitle: crystal structure of a putative mannose-6-phosphate isomerase2 (reut_a1446) from ralstonia eutropha jmp134 at 2.10 a resolution
89d2pyta1
not modelled 96.9 13 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:EutQ-like
90c3c3vA_
not modelled 96.9 18 PDB header:allergen
Chain: A: PDB Molecule:arachin arah3 isoform;
PDBTitle: crystal structure of peanut major allergen ara h 3
91d1od5a1
not modelled 96.8 12 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
92c3ehkC_
not modelled 96.8 14 PDB header:plant protein
Chain: C: PDB Molecule:prunin;
PDBTitle: crystal structure of pru du amandin, an allergenic protein2 from prunus dulcis
93c1uijA_
not modelled 96.8 14 PDB header:sugar binding protein
Chain: A: PDB Molecule:beta subunit of beta conglycinin;
PDBTitle: crystal structure of soybean beta-conglycinin beta2 homotrimer (i122m/k124w)
94d2phla1
not modelled 96.7 13 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Germin/Seed storage 7S protein
95c3s7eB_
not modelled 96.6 9 PDB header:allergen
Chain: B: PDB Molecule:allergen ara h 1, clone p41b;
PDBTitle: crystal structure of ara h 1
96d1o5ua_
not modelled 96.6 18 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Hypothetical protein TM1112
97c2bnoA_
not modelled 96.5 15 PDB header:oxidoreductase
Chain: A: PDB Molecule:epoxidase;
PDBTitle: the structure of hydroxypropylphosphonic acid epoxidase2 from s. wedmorenis.
98c3myxA_
not modelled 96.2 18 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein pspto_0244;
PDBTitle: crystal structure of a pspto_0244 (protein with unknown function which2 belongs to pfam duf861 family) from pseudomonas syringae pv. tomato3 str. dc3000 at 1.30 a resolution
99d1vr3a1
not modelled 96.2 17 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Acireductone dioxygenase
100c3ebrA_
not modelled 95.9 20 PDB header:unknown function
Chain: A: PDB Molecule:uncharacterized rmlc-like cupin;
PDBTitle: crystal structure of an rmlc-like cupin protein (reut_a0381) from2 ralstonia eutropha jmp134 at 2.60 a resolution
101c2d5fB_
not modelled 95.9 12 PDB header:plant protein
Chain: B: PDB Molecule:glycinin a3b4 subunit;
PDBTitle: crystal structure of recombinant soybean proglycinin a3b4 subunit, its2 comparison with mature glycinin a3b4 subunit, responsible for hexamer3 assembly
102c3cjxE_
not modelled 94.4 14 PDB header:unknown function
Chain: E: PDB Molecule:protein of unknown function with a cupin-like fold;
PDBTitle: crystal structure of a protein of unknown function with a cupin-like2 fold (reut_b4571) from ralstonia eutropha jmp134 at 2.60 a resolution
103c1ey2A_
not modelled 94.0 17 PDB header:oxidoreductase
Chain: A: PDB Molecule:homogentisate 1,2-dioxygenase;
PDBTitle: human homogentisate dioxygenase with fe(ii)
104d1eyba_
not modelled 93.8 17 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:Homogentisate dioxygenase
105d1sgma1
not modelled 93.8 15 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
106c3es4B_
not modelled 93.7 15 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:uncharacterized protein duf861 with a rmlc-like cupin fold;
PDBTitle: crystal structure of protein of unknown function (duf861) with a rmlc-2 like cupin fold (17741406) from agrobacterium tumefaciens str. c583 (dupont) at 1.64 a resolution
107d2bjca1
not modelled 93.7 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
108d2hsga1
not modelled 93.7 16 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
109c3iwfA_
not modelled 93.6 14 PDB header:transcription regulator
Chain: A: PDB Molecule:transcription regulator rpir family;
PDBTitle: the crystal structure of the n-terminal domain of a rpir2 transcriptional regulator from staphylococcus epidermidis to 1.4a
110d1efaa1
not modelled 93.4 14 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
111d2pa7a1
not modelled 93.4 11 Fold:Double-stranded beta-helix
Superfamily:RmlC-like cupins
Family:dTDP-sugar isomerase
112c3balB_
not modelled 93.4 15 PDB header:oxidoreductase
Chain: B: PDB Molecule:acetylacetone-cleaving enzyme;
PDBTitle: crystal structure of an acetylacetone dioxygenase from2 acinetobacter johnsonii
113c3o14B_
not modelled 93.3 19 PDB header:gene regulation
Chain: B: PDB Molecule:anti-ecfsigma factor, chrr;
PDBTitle: crystal structure of an anti-ecfsigma factor, chrr (maqu_0586) from2 marinobacter aquaeolei vt8 at 1.70 a resolution
114c3eqeB_
not modelled 93.1 15 PDB header:oxidoreductase
Chain: B: PDB Molecule:putative cystein deoxygenase;
PDBTitle: crystal structure of the yubc protein from bacillus2 subtilis. northeast structural genomics consortium target3 sr112.
115d1qpza1
not modelled 93.0 15 Fold:lambda repressor-like DNA-binding domains
Superfamily:lambda repressor-like DNA-binding domains
Family:GalR/LacI-like bacterial regulator
116d2fbqa1
not modelled 92.7 8 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
117c1sgmA_
not modelled 92.6 14 PDB header:transcription
Chain: A: PDB Molecule:putative hth-type transcriptional regulator yxaf;
PDBTitle: crystal structure of hypothetical protein yxaf
118d1jt6a1
not modelled 92.5 17 Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Tetracyclin repressor-like, N-terminal domain
119c2y0oA_
not modelled 92.4 14 PDB header:isomerase
Chain: A: PDB Molecule:probable d-lyxose ketol-isomerase;
PDBTitle: the structure of a d-lyxose isomerase from the sigmab2 regulon of bacillus subtilis
120c1u78A_
not modelled 92.4 13 PDB header:dna binding protein/dna
Chain: A: PDB Molecule:transposable element tc3 transposase;
PDBTitle: structure of the bipartite dna-binding domain of tc32 transposase bound to transposon dna

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