Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP76142
DateThu Jan 5 12:19:35 GMT 2012
Unique Job ID2b684c5152849a89

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1tjya_
Top template information
Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
Confidence and coverage
Confidence:100.0% Coverage: 93%
316 residues ( 93% 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  MTLHRFKKIALLSALGIAAISMNVQAAERIAFIPKLVGVGFFTSGGNGAQQAGKELGVDV
Secondary structure 
SS confidence 
Disorder  ????
????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  TYDGPTEPSVSGQVQLINNFVNQGYNAIIVSAVSPDGLCPALKRAMQRGVRVLTWDSDTK
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  PECRSYYINQGTPAQLGGMLVDMAARQVNKDKAKVAFFYSSPTVTDQNQWVKEAKAKIAK
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  EHPGWEIVTTQFGYNDATKSLQTAEGILKAYSDLDAIIAPDANALPAAAQAAENLKNDKV
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  AIVGFSTPNVMRPYVERGTVKEFGLWDVVQQGKISVYVADALLKKGSMKTGDKLDIKGVG
Secondary structure 
SS confidence 
Disorder 
?
?
Disorder confidence 
 
   .........310.........320.........330.........340
Sequence  QVEVSPNSVQGYDYEADGNGIVLLPERVIFNKENIGKYDF
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 1tjy chain A

3D model

Region: 25 - 340
Aligned: 316
Modelled: 316
Confidence: 100.0%
Identity: 87%
Fold: Periplasmic binding protein-like I
Superfamily: Periplasmic binding protein-like I
Family: L-arabinose binding protein-like

Phyre2

PDB 3d02 chain A

3D model

Region: 27 - 339
Aligned: 298
Modelled: 300
Confidence: 100.0%
Identity: 24%
PDB header:sugar binding protein
Chain: A: PDB Molecule:putative laci-type transcriptional regulator;
PDBTitle: crystal structure of periplasmic sugar-binding protein2 (yp_001338366.1) from klebsiella pneumoniae subsp. pneumoniae mgh3 78578 at 1.30 a resolution

Phyre2

PDB 2rjo chain A

3D model

Region: 27 - 338
Aligned: 285
Modelled: 288
Confidence: 100.0%
Identity: 15%
PDB header:signaling protein
Chain: A: PDB Molecule:twin-arginine translocation pathway signal protein;
PDBTitle: crystal structure of twin-arginine translocation pathway signal2 protein from burkholderia phytofirmans

Phyre2

PDB 3h75 chain A

3D model

Region: 29 - 338
Aligned: 281
Modelled: 282
Confidence: 100.0%
Identity: 14%
PDB header:sugar binding protein
Chain: A: PDB Molecule:periplasmic sugar-binding domain protein;
PDBTitle: crystal structure of a periplasmic sugar-binding protein from the2 pseudomonas fluorescens

Phyre2

PDB 3g1w chain B

3D model

Region: 28 - 339
Aligned: 288
Modelled: 291
Confidence: 100.0%
Identity: 18%
PDB header:transport protein
Chain: B: PDB Molecule:sugar abc transporter;
PDBTitle: crystal structure of sugar abc transporter (sugar-binding protein)2 from bacillus halodurans

Phyre2

PDB 1jx6 chain A

3D model

Region: 5 - 338
Aligned: 300
Modelled: 302
Confidence: 100.0%
Identity: 12%
Fold: Periplasmic binding protein-like I
Superfamily: Periplasmic binding protein-like I
Family: L-arabinose binding protein-like

Phyre2

PDB 3ma0 chain A

3D model

Region: 26 - 338
Aligned: 290
Modelled: 294
Confidence: 100.0%
Identity: 17%
PDB header:sugar binding protein
Chain: A: PDB Molecule:d-xylose-binding periplasmic protein;
PDBTitle: closed liganded crystal structure of xylose binding protein from2 escherichia coli

Phyre2

PDB 2qvc chain C

3D model

Region: 28 - 338
Aligned: 290
Modelled: 294
Confidence: 100.0%
Identity: 27%
PDB header:transport protein
Chain: C: PDB Molecule:sugar abc transporter, periplasmic sugar-binding
PDBTitle: crystal structure of a periplasmic sugar abc transporter2 from thermotoga maritima

Phyre2

PDB 1gca chain A

3D model

Region: 26 - 338
Aligned: 290
Modelled: 291
Confidence: 100.0%
Identity: 16%
Fold: Periplasmic binding protein-like I
Superfamily: Periplasmic binding protein-like I
Family: L-arabinose binding protein-like

Phyre2

PDB 2fvy chain A domain 1

3D model

Region: 28 - 338
Aligned: 288
Modelled: 289
Confidence: 100.0%
Identity: 17%
Fold: Periplasmic binding protein-like I
Superfamily: Periplasmic binding protein-like I
Family: L-arabinose binding protein-like

Phyre2

PDB 3o1h chain B

3D model

Region: 28 - 340
Aligned: 276
Modelled: 278
Confidence: 100.0%
Identity: 19%
PDB header:signaling protein
Chain: B: PDB Molecule:periplasmic protein tort;
PDBTitle: crystal structure of the tors sensor domain - tort complex in the2 presence of tmao

Phyre2

PDB 2x7x chain A

3D model

Region: 28 - 338
Aligned: 273
Modelled: 279
Confidence: 100.0%
Identity: 18%
PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: fructose binding periplasmic domain of hybrid two component2 system bt1754

Phyre2

PDB 3ksm chain A

3D model

Region: 29 - 301
Aligned: 271
Modelled: 273
Confidence: 100.0%
Identity: 16%
PDB header:transport protein
Chain: A: PDB Molecule:abc-type sugar transport system, periplasmic component;
PDBTitle: crystal structure of abc-type sugar transport system, periplasmic2 component from hahella chejuensis

Phyre2

PDB 1gud chain A

3D model

Region: 27 - 337
Aligned: 280
Modelled: 281
Confidence: 100.0%
Identity: 22%
Fold: Periplasmic binding protein-like I
Superfamily: Periplasmic binding protein-like I
Family: L-arabinose binding protein-like

Phyre2

PDB 8abp chain A

3D model

Region: 28 - 338
Aligned: 280
Modelled: 282
Confidence: 100.0%
Identity: 13%
Fold: Periplasmic binding protein-like I
Superfamily: Periplasmic binding protein-like I
Family: L-arabinose binding protein-like

Phyre2

PDB 3gbv chain B

3D model

Region: 26 - 339
Aligned: 280
Modelled: 272
Confidence: 100.0%
Identity: 12%
PDB header:transcription regulator
Chain: B: PDB Molecule:putative laci-family transcriptional regulator;
PDBTitle: crystal structure of a putative laci transcriptional regulator from2 bacteroides fragilis

Phyre2

PDB 2vk2 chain A

3D model

Region: 27 - 338
Aligned: 279
Modelled: 281
Confidence: 100.0%
Identity: 16%
PDB header:transport protein
Chain: A: PDB Molecule:abc transporter periplasmic-binding protein ytfq;
PDBTitle: crystal structure of a galactofuranose binding protein

Phyre2

PDB 3l6u chain A

3D model

Region: 30 - 331
Aligned: 268
Modelled: 267
Confidence: 100.0%
Identity: 14%
PDB header:transport protein
Chain: A: PDB Molecule:abc-type sugar transport system periplasmic
PDBTitle: crystal structure of abc-type sugar transport system,2 periplasmic component from exiguobacterium sibiricum

Phyre2

PDB 3rot chain A

3D model

Region: 28 - 296
Aligned: 265
Modelled: 268
Confidence: 100.0%
Identity: 15%
PDB header:transport protein
Chain: A: PDB Molecule:abc sugar transporter, periplasmic sugar binding protein;
PDBTitle: crystal structure of abc sugar transporter (periplasmic sugar binding2 protein) from legionella pneumophila

Phyre2

PDB 3brs chain A

3D model

Region: 28 - 333
Aligned: 266
Modelled: 275
Confidence: 100.0%
Identity: 19%
PDB header:transport protein
Chain: A: PDB Molecule:periplasmic binding protein/laci transcriptional regulator;
PDBTitle: crystal structure of sugar transporter from clostridium2 phytofermentans

Phyre2

PDB 2zau chain A domain 1

3D model

Region: 8 - 61
Aligned: 54
Modelled: 54
Confidence: 67.9%
Identity: 13%
Fold: Bacillus chorismate mutase-like
Superfamily: PurM N-terminal domain-like
Family: PurM N-terminal domain-like

Phyre2
1
d1tjya_
2
c3d02A_
3
c2rjoA_
4
c3h75A_
5
c3g1wB_
6
d1jx6a_
7
c3ma0A_
8
c2qvcC_
9
d1gcaa_
10
d2fvya1
11
c3o1hB_
12
c2x7xA_
13
c3ksmA_
14
d1guda_
15
d8abpa_
16
c3gbvB_
17
c2vk2A_
18
c3l6uA_
19
c3rotA_
20
c3brsA_
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
d2zaua1
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



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1tjya_
100.0 87 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
2c3d02A_
100.0 24 PDB header:sugar binding protein
Chain: A: PDB Molecule:putative laci-type transcriptional regulator;
PDBTitle: crystal structure of periplasmic sugar-binding protein2 (yp_001338366.1) from klebsiella pneumoniae subsp. pneumoniae mgh3 78578 at 1.30 a resolution
3c2rjoA_
100.0 15 PDB header:signaling protein
Chain: A: PDB Molecule:twin-arginine translocation pathway signal protein;
PDBTitle: crystal structure of twin-arginine translocation pathway signal2 protein from burkholderia phytofirmans
4c3h75A_
100.0 14 PDB header:sugar binding protein
Chain: A: PDB Molecule:periplasmic sugar-binding domain protein;
PDBTitle: crystal structure of a periplasmic sugar-binding protein from the2 pseudomonas fluorescens
5c3g1wB_
100.0 18 PDB header:transport protein
Chain: B: PDB Molecule:sugar abc transporter;
PDBTitle: crystal structure of sugar abc transporter (sugar-binding protein)2 from bacillus halodurans
6d1jx6a_
100.0 12 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
7c3ma0A_
100.0 17 PDB header:sugar binding protein
Chain: A: PDB Molecule:d-xylose-binding periplasmic protein;
PDBTitle: closed liganded crystal structure of xylose binding protein from2 escherichia coli
8c2qvcC_
100.0 27 PDB header:transport protein
Chain: C: PDB Molecule:sugar abc transporter, periplasmic sugar-binding
PDBTitle: crystal structure of a periplasmic sugar abc transporter2 from thermotoga maritima
9d1gcaa_
100.0 16 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
10d2fvya1
100.0 17 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
11c3o1hB_
100.0 19 PDB header:signaling protein
Chain: B: PDB Molecule:periplasmic protein tort;
PDBTitle: crystal structure of the tors sensor domain - tort complex in the2 presence of tmao
12c2x7xA_
100.0 18 PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: fructose binding periplasmic domain of hybrid two component2 system bt1754
13c3ksmA_
100.0 16 PDB header:transport protein
Chain: A: PDB Molecule:abc-type sugar transport system, periplasmic component;
PDBTitle: crystal structure of abc-type sugar transport system, periplasmic2 component from hahella chejuensis
14d1guda_
100.0 22 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
15d8abpa_
100.0 13 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
16c3gbvB_
100.0 12 PDB header:transcription regulator
Chain: B: PDB Molecule:putative laci-family transcriptional regulator;
PDBTitle: crystal structure of a putative laci transcriptional regulator from2 bacteroides fragilis
17c2vk2A_
100.0 16 PDB header:transport protein
Chain: A: PDB Molecule:abc transporter periplasmic-binding protein ytfq;
PDBTitle: crystal structure of a galactofuranose binding protein
18c3l6uA_
100.0 14 PDB header:transport protein
Chain: A: PDB Molecule:abc-type sugar transport system periplasmic
PDBTitle: crystal structure of abc-type sugar transport system,2 periplasmic component from exiguobacterium sibiricum
19c3rotA_
100.0 15 PDB header:transport protein
Chain: A: PDB Molecule:abc sugar transporter, periplasmic sugar binding protein;
PDBTitle: crystal structure of abc sugar transporter (periplasmic sugar binding2 protein) from legionella pneumophila
20c3brsA_
100.0 19 PDB header:transport protein
Chain: A: PDB Molecule:periplasmic binding protein/laci transcriptional regulator;
PDBTitle: crystal structure of sugar transporter from clostridium2 phytofermentans
21c3l49D_
not modelled 100.0 17 PDB header:transport protein
Chain: D: PDB Molecule:abc sugar (ribose) transporter, periplasmic
PDBTitle: crystal structure of abc sugar transporter subunit from2 rhodobacter sphaeroides 2.4.1
22c2fn9A_
not modelled 100.0 17 PDB header:sugar binding protein
Chain: A: PDB Molecule:ribose abc transporter, periplasmic ribose-binding protein;
PDBTitle: thermotoga maritima ribose binding protein unliganded form
23c2ioyB_
not modelled 100.0 23 PDB header:sugar binding protein
Chain: B: PDB Molecule:periplasmic sugar-binding protein;
PDBTitle: crystal structure of thermoanaerobacter tengcongensis2 ribose binding protein
24d2dria_
not modelled 100.0 20 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
25c3d8uA_
not modelled 100.0 12 PDB header:transcription regulator
Chain: A: PDB Molecule:purr transcriptional regulator;
PDBTitle: the crystal structure of a purr family transcriptional regulator from2 vibrio parahaemolyticus rimd 2210633
26c3h5oB_
not modelled 100.0 9 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator gntr;
PDBTitle: the crystal structure of transcription regulator gntr from2 chromobacterium violaceum
27c2rgyA_
not modelled 100.0 6 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of transcriptional regulator of laci family from2 burkhoderia phymatum
28c3mizB_
not modelled 100.0 12 PDB header:transcription regulator
Chain: B: PDB Molecule:putative transcriptional regulator protein, laci
PDBTitle: crystal structure of a putative transcriptional regulator2 protein, lacl family from rhizobium etli
29c2iksA_
not modelled 100.0 13 PDB header:transcription
Chain: A: PDB Molecule:dna-binding transcriptional dual regulator;
PDBTitle: crystal structure of n-terminal truncated dna-binding transcriptional2 dual regulator from escherichia coli k12
30c3e3mA_
not modelled 100.0 12 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a laci family transcriptional2 regulator from silicibacter pomeroyi
31c3k4hA_
not modelled 100.0 8 PDB header:transcription regulator
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of putative transcriptional regulator laci from2 bacillus cereus subsp. cytotoxis nvh 391-98
32c3brqA_
not modelled 100.0 12 PDB header:transcription regulator
Chain: A: PDB Molecule:hth-type transcriptional regulator ascg;
PDBTitle: crystal structure of the escherichia coli transcriptional repressor2 ascg
33c3hcwB_
not modelled 100.0 11 PDB header:rna binding protein
Chain: B: PDB Molecule:maltose operon transcriptional repressor;
PDBTitle: crystal structure of probable maltose operon transcriptional repressor2 malr from staphylococcus areus
34d2nzug1
not modelled 100.0 12 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
35c3c3kA_
not modelled 100.0 12 PDB header:isomerase
Chain: A: PDB Molecule:alanine racemase;
PDBTitle: crystal structure of an uncharacterized protein from actinobacillus2 succinogenes
36c3dbiA_
not modelled 100.0 12 PDB header:transcription regulator
Chain: A: PDB Molecule:sugar-binding transcriptional regulator, laci family;
PDBTitle: crystal structure of sugar-binding transcriptional regulator (laci2 family) from escherichia coli complexed with phosphate
37c3kkeA_
not modelled 100.0 17 PDB header:transcription regulator
Chain: A: PDB Molecule:laci family transcriptional regulator;
PDBTitle: crystal structure of a laci family transcriptional regulator2 from mycobacterium smegmatis
38c1jyeA_
not modelled 100.0 13 PDB header:transcription
Chain: A: PDB Molecule:lactose operon repressor;
PDBTitle: structure of a dimeric lac repressor with c-terminal deletion and k84l2 substitution
39d1jyea_
not modelled 100.0 13 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
40c3gv0A_
not modelled 100.0 11 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of laci family transcription regulator from2 agrobacterium tumefaciens
41c3g85A_
not modelled 100.0 10 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator (laci family);
PDBTitle: crystal structure of laci family transcription regulator from2 clostridium acetobutylicum
42c3qk7C_
not modelled 100.0 13 PDB header:transcription regulator
Chain: C: PDB Molecule:transcriptional regulators;
PDBTitle: crystal structure of putative transcriptional regulator from yersinia2 pestis biovar microtus str. 91001
43c3hs3A_
not modelled 100.0 15 PDB header:transcription regulator
Chain: A: PDB Molecule:ribose operon repressor;
PDBTitle: crystal structure of periplasmic binding ribose operon2 repressor protein from lactobacillus acidophilus
44c3jy6B_
not modelled 100.0 12 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of laci transcriptional regulator from lactobacillus2 brevis
45c3egcF_
not modelled 100.0 12 PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:putative ribose operon repressor;
PDBTitle: crystal structure of a putative ribose operon repressor from2 burkholderia thailandensis
46c2fqxA_
not modelled 100.0 10 PDB header:transport protein
Chain: A: PDB Molecule:membrane lipoprotein tmpc;
PDBTitle: pnra from treponema pallidum complexed with guanosine
47c3bblA_
not modelled 100.0 9 PDB header:regulatory protein
Chain: A: PDB Molecule:regulatory protein of laci family;
PDBTitle: crystal structure of a regulatory protein of laci family from2 chloroflexus aggregans
48c2qu7B_
not modelled 100.0 16 PDB header:transcription
Chain: B: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of a putative transcription regulator2 from staphylococcus saprophyticus subsp. saprophyticus
49c2o20H_
not modelled 100.0 10 PDB header:transcription
Chain: H: PDB Molecule:catabolite control protein a;
PDBTitle: crystal structure of transcription regulator ccpa of lactococcus2 lactis
50c3o74A_
not modelled 100.0 13 PDB header:transcription
Chain: A: PDB Molecule:fructose transport system repressor frur;
PDBTitle: crystal structure of cra transcriptional dual regulator from2 pseudomonas putida
51d1dbqa_
not modelled 100.0 8 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
52c3ctpB_
not modelled 100.0 14 PDB header:transcription regulator
Chain: B: PDB Molecule:periplasmic binding protein/laci transcriptional regulator;
PDBTitle: crystal structure of periplasmic binding protein/laci transcriptional2 regulator from alkaliphilus metalliredigens qymf complexed with d-3 xylulofuranose
53d1tlfa_
not modelled 100.0 12 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
54c3cs3A_
not modelled 100.0 11 PDB header:transcription regulator
Chain: A: PDB Molecule:sugar-binding transcriptional regulator, laci family;
PDBTitle: crystal structure of sugar-binding transcriptional regulator (laci2 family) from enterococcus faecalis
55c3k9cA_
not modelled 100.0 11 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, laci family protein;
PDBTitle: crystal structure of laci transcriptional regulator from rhodococcus2 species.
56c1zvvA_
not modelled 100.0 13 PDB header:transcription/dna
Chain: A: PDB Molecule:glucose-resistance amylase regulator;
PDBTitle: crystal structure of a ccpa-crh-dna complex
57c3clkB_
not modelled 100.0 13 PDB header:transcription regulator
Chain: B: PDB Molecule:transcription regulator;
PDBTitle: crystal structure of a transcription regulator from lactobacillus2 plantarum
58c2hqbA_
not modelled 100.0 14 PDB header:transcription
Chain: A: PDB Molecule:transcriptional activator of comk gene;
PDBTitle: crystal structure of a transcriptional activator of comk2 gene from bacillus halodurans
59c2h0aA_
not modelled 99.9 13 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator;
PDBTitle: crystal structure of probable transcription regulator from2 thermus thermophilus
60d1byka_
not modelled 99.9 8 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
61c3lftA_
not modelled 99.9 15 PDB header:structure genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: the crystal structure of the abc domain in complex with l-trp from2 streptococcus pneumonia to 1.35a
62c3s99A_
not modelled 99.9 13 PDB header:lipid binding protein
Chain: A: PDB Molecule:basic membrane lipoprotein;
PDBTitle: crystal structure of a basic membrane lipoprotein from brucella2 melitensis, iodide soak
63c2qh8A_
not modelled 99.9 18 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of conserved domain protein from vibrio2 cholerae o1 biovar eltor str. n16961
64c3bilA_
not modelled 99.9 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:probable laci-family transcriptional regulator;
PDBTitle: crystal structure of a probable laci family transcriptional2 regulator from corynebacterium glutamicum
65c3jvdA_
not modelled 99.9 14 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulators;
PDBTitle: crystal structure of putative transcription regulation repressor (laci2 family) from corynebacterium glutamicum
66c3huuC_
not modelled 99.9 12 PDB header:transcription regulator
Chain: C: PDB Molecule:transcription regulator like protein;
PDBTitle: crystal structure of transcription regulator like protein from2 staphylococcus haemolyticus
67c3gybB_
not modelled 99.9 11 PDB header:transcription regulator
Chain: B: PDB Molecule:transcriptional regulators (laci-family
PDBTitle: crystal structure of a laci-family transcriptional2 regulatory protein from corynebacterium glutamicum
68c3e61A_
not modelled 99.9 15 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative transcriptional repressor of ribose operon;
PDBTitle: crystal structure of a putative transcriptional repressor of ribose2 operon from staphylococcus saprophyticus subsp. saprophyticus
69c1bdhA_
not modelled 99.9 11 PDB header:transcription/dna
Chain: A: PDB Molecule:protein (purine repressor);
PDBTitle: purine repressor mutant-hypoxanthine-palindromic operator2 complex
70c3kjxD_
not modelled 99.9 10 PDB header:transcription regulator
Chain: D: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from silicibacter pomeroyi
71c3h5tA_
not modelled 99.8 12 PDB header:transcription regulator
Chain: A: PDB Molecule:transcriptional regulator, laci family;
PDBTitle: crystal structure of a transcriptional regulator, lacl2 family protein from corynebacterium glutamicum
72c3i09A_
not modelled 99.1 11 PDB header:transport protein
Chain: A: PDB Molecule:periplasmic branched-chain amino acid-binding protein;
PDBTitle: crystal structure of a periplasmic binding protein (bma2936) from2 burkholderia mallei at 1.80 a resolution
73c3i45A_
not modelled 99.1 16 PDB header:signaling protein
Chain: A: PDB Molecule:twin-arginine translocation pathway signal protein;
PDBTitle: crystal structure of putative twin-arginine translocation pathway2 signal protein from rhodospirillum rubrum atcc 11170
74c3qi7A_
not modelled 99.1 13 PDB header:transcription
Chain: A: PDB Molecule:putative transcriptional regulator;
PDBTitle: crystal structure of a putative transcriptional regulator2 (yp_001089212.1) from clostridium difficile 630 at 1.86 a resolution
75c3sg0A_
not modelled 99.1 14 PDB header:signaling protein
Chain: A: PDB Molecule:extracellular ligand-binding receptor;
PDBTitle: the crystal structure of an extracellular ligand-binding receptor from2 rhodopseudomonas palustris haa2
76c3snrA_
not modelled 99.1 11 PDB header:transport protein
Chain: A: PDB Molecule:extracellular ligand-binding receptor;
PDBTitle: rpd_1889 protein, an extracellular ligand-binding receptor from2 rhodopseudomonas palustris.
77c3eafA_
not modelled 99.0 11 PDB header:transport protein
Chain: A: PDB Molecule:abc transporter, substrate binding protein;
PDBTitle: crystal structure of abc transporter, substrate binding protein2 aeropyrum pernix
78d2liva_
not modelled 99.0 13 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
79d1qo0a_
not modelled 99.0 13 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
80c3lkbB_
not modelled 99.0 14 PDB header:transport protein
Chain: B: PDB Molecule:probable branched-chain amino acid abc
PDBTitle: crystal structure of a branched chain amino acid abc2 transporter from thermus thermophilus with bound valine
81c3t0nA_
not modelled 98.9 16 PDB header:signaling protein
Chain: A: PDB Molecule:twin-arginine translocation pathway signal;
PDBTitle: crystal structure of twin-arginine translocation pathway signal from2 rhodopseudomonas palustris bisb5
82c3hutA_
not modelled 98.8 11 PDB header:transport protein
Chain: A: PDB Molecule:putative branched-chain amino acid abc
PDBTitle: crystal structure of a putative branched-chain amino acid2 abc transporter from rhodospirillum rubrum
83c3n0wA_
not modelled 98.8 9 PDB header:transport protein
Chain: A: PDB Molecule:abc branched chain amino acid family transporter,
PDBTitle: crystal structure of a branched chain amino acid abc transporter2 periplasmic ligand-binding protein (bxe_c0949) from burkholderia3 xenovorans lb400 at 1.88 a resolution
84c3ip5A_
not modelled 98.8 17 PDB header:transport protein
Chain: A: PDB Molecule:abc transporter, substrate binding protein (amino acid);
PDBTitle: structure of atu2422-gaba receptor in complex with alanine
85c3h5lB_
not modelled 98.7 10 PDB header:transport protein
Chain: B: PDB Molecule:putative branched-chain amino acid abc
PDBTitle: crystal structure of a putative branched-chain amino acid2 abc transporter from silicibacter pomeroyi
86c3td9A_
not modelled 98.7 16 PDB header:transport protein
Chain: A: PDB Molecule:branched chain amino acid abc transporter, periplasmic
PDBTitle: crystal structure of a leucine binding protein livk (tm1135) from2 thermotoga maritima msb8 at 1.90 a resolution
87d1usga_
not modelled 98.7 13 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
88c3lopA_
not modelled 98.6 8 PDB header:substrate binding protein
Chain: A: PDB Molecule:substrate binding periplasmic protein;
PDBTitle: crystal structure of substrate-binding periplasmic protein2 (pbp) from ralstonia solanacearum
89d3ckma1
not modelled 98.6 12 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
90c3sajB_
not modelled 98.2 8 PDB header:transport protein
Chain: B: PDB Molecule:glutamate receptor 1;
PDBTitle: crystal structure of glutamate receptor glua1 amino terminal domain
91c3n0xA_
not modelled 98.2 14 PDB header:transport protein
Chain: A: PDB Molecule:possible substrate binding protein of abc transporter
PDBTitle: crystal structure of an abc-type branched-chain amino acid transporter2 (rpa4397) from rhodopseudomonas palustris cga009 at 1.50 a resolution
92c3h6hB_
not modelled 98.1 12 PDB header:membrane protein
Chain: B: PDB Molecule:glutamate receptor, ionotropic kainate 2;
PDBTitle: crystal structure of the glur6 amino terminal domain dimer assembly2 mpd form
93d1jdpa_
not modelled 98.0 12 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
94c1jdpA_
not modelled 98.0 12 PDB header:signaling protein
Chain: A: PDB Molecule:atrial natriuretic peptide clearance receptor;
PDBTitle: crystal structure of hormone/receptor complex
95d1ewka_
not modelled 98.0 8 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
96c1yk1B_
not modelled 97.9 11 PDB header:hormone/growth factor receptor
Chain: B: PDB Molecule:atrial natriuretic peptide clearance receptor;
PDBTitle: structure of natriuretic peptide receptor-c complexed with brain2 natriuretic peptide
97c3q41B_
not modelled 97.9 12 PDB header:transport protein
Chain: B: PDB Molecule:glutamate [nmda] receptor subunit zeta-1;
PDBTitle: crystal structure of the glun1 n-terminal domain (ntd)
98c2wjxA_
not modelled 97.8 9 PDB header:transport protein
Chain: A: PDB Molecule:glutamate receptor 2;
PDBTitle: crystal structure of the human ionotropic glutamate2 receptor glur2 atd region at 4.1 a resolution
99c3p3wC_
not modelled 97.7 8 PDB header:transport protein
Chain: C: PDB Molecule:glutamate receptor 3;
PDBTitle: structure of a dimeric glua3 n-terminal domain (ntd) at 4.2 a2 resolution
100c3sm9A_
not modelled 97.2 10 PDB header:signaling protein
Chain: A: PDB Molecule:metabotropic glutamate receptor 3;
PDBTitle: crystal structure of metabotropic glutamate receptor 3 precursor in2 presence of ly341495 antagonist
101c3kg2A_
not modelled 97.0 9 PDB header:membrane protein, transport protein
Chain: A: PDB Molecule:glutamate receptor 2;
PDBTitle: ampa subtype ionotropic glutamate receptor in complex with competitive2 antagonist zk 200775
102c3om1A_
not modelled 96.8 10 PDB header:membrane protein
Chain: A: PDB Molecule:glutamate receptor gluk5 (ka2);
PDBTitle: crystal structure of the gluk5 (ka2) atd dimer at 1.7 angstrom2 resolution
103d1dp4a_
not modelled 96.7 12 Fold:Periplasmic binding protein-like I
Superfamily:Periplasmic binding protein-like I
Family:L-arabinose binding protein-like
104c2uygF_
not modelled 96.0 14 PDB header:lyase
Chain: F: PDB Molecule:3-dehydroquinate dehydratase;
PDBTitle: crystallogaphic structure of the typeii 3-dehydroquinase2 from thermus thermophilus
105d2c4va1
not modelled 95.0 16 Fold:Flavodoxin-like
Superfamily:Type II 3-dehydroquinate dehydratase
Family:Type II 3-dehydroquinate dehydratase
106c2e4wA_
not modelled 94.9 8 PDB header:signaling protein
Chain: A: PDB Molecule:metabotropic glutamate receptor 3;
PDBTitle: crystal structure of the extracellular region of the group ii2 metabotropic glutamate receptor complexed with 1s,3s-acpd
107d1gtza_
not modelled 94.8 14 Fold:Flavodoxin-like
Superfamily:Type II 3-dehydroquinate dehydratase
Family:Type II 3-dehydroquinate dehydratase
108d1gqoa_
not modelled 94.6 13 Fold:Flavodoxin-like
Superfamily:Type II 3-dehydroquinate dehydratase
Family:Type II 3-dehydroquinate dehydratase
109c3lwzC_
not modelled 94.0 4 PDB header:lyase
Chain: C: PDB Molecule:3-dehydroquinate dehydratase;
PDBTitle: 1.65 angstrom resolution crystal structure of type ii 3-2 dehydroquinate dehydratase (aroq) from yersinia pestis
110c3nvaB_
not modelled 93.4 18 PDB header:ligase
Chain: B: PDB Molecule:ctp synthase;
PDBTitle: dimeric form of ctp synthase from sulfolobus solfataricus
111c3n8kG_
not modelled 93.2 10 PDB header:lyase
Chain: G: PDB Molecule:3-dehydroquinate dehydratase;
PDBTitle: type ii dehydroquinase from mycobacterium tuberculosis complexed with2 citrazinic acid
112c2l2qA_
not modelled 93.1 11 PDB header:transferase
Chain: A: PDB Molecule:pts system, cellobiose-specific iib component (cela);
PDBTitle: solution structure of cellobiose-specific phosphotransferase iib2 component protein from borrelia burgdorferi
113d1h05a_
not modelled 93.0 9 Fold:Flavodoxin-like
Superfamily:Type II 3-dehydroquinate dehydratase
Family:Type II 3-dehydroquinate dehydratase
114d1uqra_
not modelled 92.8 11 Fold:Flavodoxin-like
Superfamily:Type II 3-dehydroquinate dehydratase
Family:Type II 3-dehydroquinate dehydratase
115c2dc1A_
not modelled 92.5 14 PDB header:oxidoreductase
Chain: A: PDB Molecule:l-aspartate dehydrogenase;
PDBTitle: crystal structure of l-aspartate dehydrogenase from2 hyperthermophilic archaeon archaeoglobus fulgidus
116c3kipU_
not modelled 92.2 10 PDB header:lyase
Chain: U: PDB Molecule:3-dehydroquinase, type ii;
PDBTitle: crystal structure of type-ii 3-dehydroquinase from c. albicans
117d1vcoa1
not modelled 92.1 20 Fold:Flavodoxin-like
Superfamily:Class I glutamine amidotransferase-like
Family:Class I glutamine amidotransferases (GAT)
118c3u80A_
not modelled 90.5 11 PDB header:unknown function
Chain: A: PDB Molecule:3-dehydroquinate dehydratase, type ii;
PDBTitle: 1.60 angstrom resolution crystal structure of a 3-dehydroquinate2 dehydratase-like protein from bifidobacterium longum
119c1vcnA_
not modelled 89.8 19 PDB header:ligase
Chain: A: PDB Molecule:ctp synthetase;
PDBTitle: crystal structure of t.th. hb8 ctp synthetase complex with sulfate2 anion
120c2e4zA_
not modelled 89.3 10 PDB header:signaling protein
Chain: A: PDB Molecule:metabotropic glutamate receptor 7;
PDBTitle: crystal structure of the ligand-binding region of the group iii2 metabotropic glutamate receptor

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