Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP76261
DateThu Jan 5 12:21:20 GMT 2012
Unique Job ID80c00a00b326baaf

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c3pjwA_
Top template information
PDB header:lyase
Chain: A: PDB Molecule:cyclic dimeric gmp binding protein;
PDBTitle: structure of pseudomonas fluorescence lapd ggdef-eal dual domain, i23
Confidence and coverage
Confidence:100.0% Coverage: 78%
417 residues ( 78% 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  MQKAQRIIKTYRRNRMIVCTICALVTLASTLSVRFISQRNLNQQRVVQFANHAVEELDKV
Secondary structure 
SS confidence 
Disorder  ??
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  LLPLQAGSEVLLPLIGLPCSVAHLPLRKQAAKLQTVRSIGLVQDGTLYCSSIFGYRNVPV
Secondary structure 
SS confidence 
Disorder 
?????
????
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  VDILAELPAPQPLLRLTIDRALIKGSPVLIQWTPAAGSSNAGVMEMINIDLLTAMLLEPQ
Secondary structure 
SS confidence 
Disorder 
?
?
??
?
??????????????
?????
???
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  LPQISSASLTVDKRHLLYGNGLVDSLPQPEDNENYQVSSQRFPFTINVNGPGATALAWHY
Secondary structure 
SS confidence 
Disorder  ????
?
?????????????????
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  LPTQLPLAVLLSLLVGYIAWLATAYRMSFSREINLGLAQHEFELFCQPLLNARSQQCIGV
Secondary structure 
SS confidence 
Disorder 
Disorder confidence 
 
   .........310.........320.........330.........340.........350.........360
Sequence  EILLRWNNPRQGWISPDVFIPIAEEHHLIVPLTRYVMAETIRQRHVFPMSSQFHVGINVA
Secondary structure 
SS confidence 
Disorder 
??
Disorder confidence 
 
   .........370.........380.........390.........400.........410.........420
Sequence  PSHFRRGVLIKDLNQYWFSAHPIQQLILEITERDALLDVDYRIARELHRKNVKLAIDDFG
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........430.........440.........450.........460.........470.........480
Sequence  TGNSSFSWLETLRPDVLKIDKSFTAAIGSDAVNSTVTDIIIALGQRLNIELVAEGVETQE
Secondary structure 
SS confidence 
Disorder 
????
Disorder confidence 
 
   .........490.........500.........510.........520.........530..
Sequence  QAKYLRRHGVHILQGYLYAQPMPLRDFPKWLAGSQPPPARHNGHITPIMPLR
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 3pjw chain A

3D model

Region: 60 - 504
Aligned: 417
Modelled: 445
Confidence: 100.0%
Identity: 17%
PDB header:lyase
Chain: A: PDB Molecule:cyclic dimeric gmp binding protein;
PDBTitle: structure of pseudomonas fluorescence lapd ggdef-eal dual domain, i23

Phyre2

PDB 3hvb chain B

3D model

Region: 265 - 507
Aligned: 242
Modelled: 243
Confidence: 100.0%
Identity: 23%
PDB header:hydrolase
Chain: B: PDB Molecule:protein fimx;
PDBTitle: crystal structure of the dual-domain ggdef-eal module of2 fimx from pseudomonas aeruginosa

Phyre2

PDB 3hv9 chain A

3D model

Region: 262 - 507
Aligned: 245
Modelled: 246
Confidence: 100.0%
Identity: 24%
PDB header:hydrolase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx eal domain from pseudomonas aeruginosa

Phyre2

PDB 3gfz chain B

3D model

Region: 114 - 501
Aligned: 340
Modelled: 355
Confidence: 100.0%
Identity: 17%
PDB header:hydrolase, signaling protein
Chain: B: PDB Molecule:klebsiella pneumoniae blrp1;
PDBTitle: klebsiella pneumoniae blrp1 ph 6 manganese/cy-digmp complex

Phyre2

PDB 3s83 chain A

3D model

Region: 269 - 518
Aligned: 247
Modelled: 250
Confidence: 100.0%
Identity: 30%
PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15

Phyre2

PDB 3pfm chain A

3D model

Region: 264 - 504
Aligned: 237
Modelled: 241
Confidence: 100.0%
Identity: 22%
PDB header:signaling protein
Chain: A: PDB Molecule:ggdef domain protein;
PDBTitle: crystal structure of a eal domain of ggdef domain protein from2 pseudomonas fluorescens pf

Phyre2

PDB 2w27 chain A

3D model

Region: 273 - 503
Aligned: 226
Modelled: 231
Confidence: 100.0%
Identity: 19%
PDB header:signaling protein
Chain: A: PDB Molecule:ykui protein;
PDBTitle: crystal structure of the bacillus subtilis ykui protein,2 with an eal domain, in complex with substrate c-di-gmp and3 calcium

Phyre2

PDB 2r6o chain B

3D model

Region: 268 - 517
Aligned: 238
Modelled: 238
Confidence: 100.0%
Identity: 28%
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative diguanylate cyclase/phosphodiesterase (ggdef & eal
PDBTitle: crystal structure of putative diguanylate cyclase/phosphodiesterase2 from thiobacillus denitrificans

Phyre2

PDB 2bas chain A domain 1

3D model

Region: 272 - 520
Aligned: 245
Modelled: 249
Confidence: 100.0%
Identity: 18%
Fold: TIM beta/alpha-barrel
Superfamily: EAL domain-like
Family: EAL domain

Phyre2

PDB 3kzp chain A

3D model

Region: 281 - 503
Aligned: 219
Modelled: 223
Confidence: 100.0%
Identity: 22%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative diguanylate cyclase/phosphodiesterase;
PDBTitle: crystal structure of putative diguanylate cyclase/phosphodiesterase2 from listaria monocytigenes

Phyre2

PDB 1w25 chain B

3D model

Region: 54 - 256
Aligned: 194
Modelled: 203
Confidence: 98.3%
Identity: 6%
PDB header:signaling protein
Chain: B: PDB Molecule:stalked-cell differentiation controlling protein;
PDBTitle: response regulator pled in complex with c-digmp

Phyre2

PDB 3ezu chain A

3D model

Region: 62 - 254
Aligned: 175
Modelled: 193
Confidence: 97.8%
Identity: 10%
PDB header:signaling protein
Chain: A: PDB Molecule:ggdef domain protein;
PDBTitle: crystal structure of multidomain protein of unknown function with2 ggdef-domain (np_951600.1) from geobacter sulfurreducens at 1.95 a3 resolution

Phyre2

PDB 3bre chain A

3D model

Region: 33 - 256
Aligned: 210
Modelled: 224
Confidence: 97.3%
Identity: 9%
PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702

Phyre2

PDB 3i5c chain A

3D model

Region: 48 - 255
Aligned: 194
Modelled: 208
Confidence: 97.3%
Identity: 10%
PDB header:signaling protein
Chain: A: PDB Molecule:fusion of general control protein gcn4 and wspr response
PDBTitle: crystal structure of a fusion protein containing the leucine zipper of2 gcn4 and the ggdef domain of wspr from pseudomonas aeruginosa

Phyre2

PDB 3i5a chain A

3D model

Region: 33 - 253
Aligned: 206
Modelled: 221
Confidence: 97.0%
Identity: 8%
PDB header:signaling protein
Chain: A: PDB Molecule:response regulator/ggdef domain protein;
PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae

Phyre2

PDB 3i5b chain A

3D model

Region: 87 - 256
Aligned: 166
Modelled: 170
Confidence: 96.8%
Identity: 7%
PDB header:signaling protein
Chain: A: PDB Molecule:wspr response regulator;
PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa

Phyre2

PDB 3icl chain A

3D model

Region: 88 - 256
Aligned: 160
Modelled: 164
Confidence: 96.7%
Identity: 9%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:eal/ggdef domain protein;
PDBTitle: x-ray structure of protein (eal/ggdef domain protein) from2 m.capsulatus, northeast structural genomics consortium3 target mcr174c

Phyre2

PDB 3mtk chain A

3D model

Region: 82 - 256
Aligned: 156
Modelled: 175
Confidence: 96.2%
Identity: 9%
PDB header:transferase
Chain: A: PDB Molecule:diguanylate cyclase/phosphodiesterase;
PDBTitle: x-ray structure of diguanylate cyclase/phosphodiesterase from2 caldicellulosiruptor saccharolyticus, northeast structural genomics3 consortium target clr27c

Phyre2

PDB 1w25 chain A domain 3

3D model

Region: 86 - 256
Aligned: 160
Modelled: 171
Confidence: 96.0%
Identity: 4%
Fold: Ferredoxin-like
Superfamily: Nucleotide cyclase
Family: GGDEF domain

Phyre2

PDB 3ign chain A

3D model

Region: 87 - 254
Aligned: 159
Modelled: 168
Confidence: 95.9%
Identity: 8%
PDB header:transferase
Chain: A: PDB Molecule:diguanylate cyclase;
PDBTitle: crystal structure of the ggdef domain from marinobacter2 aquaeolei diguanylate cyclase complexed with c-di-gmp -3 northeast structural genomics consortium target mqr89a

Phyre2
1
c3pjwA_
2
c3hvbB_
3
c3hv9A_
4
c3gfzB_
5
c3s83A_
6
c3pfmA_
7
c2w27A_
8
c2r6oB_
9
d2basa1
10
c3kzpA_
11
c1w25B_
12
c3ezuA_
13
c3breA_
14
c3i5cA_
15
c3i5aA_
16
c3i5bA_
17
c3iclA_
18
c3mtkA_
19
d1w25a3
20
c3ignA_
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



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3pjwA_
100.0 17 PDB header:lyase
Chain: A: PDB Molecule:cyclic dimeric gmp binding protein;
PDBTitle: structure of pseudomonas fluorescence lapd ggdef-eal dual domain, i23
2c3hvbB_
100.0 23 PDB header:hydrolase
Chain: B: PDB Molecule:protein fimx;
PDBTitle: crystal structure of the dual-domain ggdef-eal module of2 fimx from pseudomonas aeruginosa
3c3hv9A_
100.0 24 PDB header:hydrolase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx eal domain from pseudomonas aeruginosa
4c3gfzB_
100.0 17 PDB header:hydrolase, signaling protein
Chain: B: PDB Molecule:klebsiella pneumoniae blrp1;
PDBTitle: klebsiella pneumoniae blrp1 ph 6 manganese/cy-digmp complex
5c3s83A_
100.0 30 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15
6c3pfmA_
100.0 22 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef domain protein;
PDBTitle: crystal structure of a eal domain of ggdef domain protein from2 pseudomonas fluorescens pf
7c2w27A_
100.0 19 PDB header:signaling protein
Chain: A: PDB Molecule:ykui protein;
PDBTitle: crystal structure of the bacillus subtilis ykui protein,2 with an eal domain, in complex with substrate c-di-gmp and3 calcium
8c2r6oB_
100.0 28 PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:putative diguanylate cyclase/phosphodiesterase (ggdef & eal
PDBTitle: crystal structure of putative diguanylate cyclase/phosphodiesterase2 from thiobacillus denitrificans
9d2basa1
100.0 18 Fold:TIM beta/alpha-barrel
Superfamily:EAL domain-like
Family:EAL domain
10c3kzpA_
100.0 22 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative diguanylate cyclase/phosphodiesterase;
PDBTitle: crystal structure of putative diguanylate cyclase/phosphodiesterase2 from listaria monocytigenes
11c1w25B_
98.3 6 PDB header:signaling protein
Chain: B: PDB Molecule:stalked-cell differentiation controlling protein;
PDBTitle: response regulator pled in complex with c-digmp
12c3ezuA_
97.8 10 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef domain protein;
PDBTitle: crystal structure of multidomain protein of unknown function with2 ggdef-domain (np_951600.1) from geobacter sulfurreducens at 1.95 a3 resolution
13c3breA_
97.3 9 PDB header:signaling protein
Chain: A: PDB Molecule:probable two-component response regulator;
PDBTitle: crystal structure of p.aeruginosa pa3702
14c3i5cA_
97.3 10 PDB header:signaling protein
Chain: A: PDB Molecule:fusion of general control protein gcn4 and wspr response
PDBTitle: crystal structure of a fusion protein containing the leucine zipper of2 gcn4 and the ggdef domain of wspr from pseudomonas aeruginosa
15c3i5aA_
97.0 8 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator/ggdef domain protein;
PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae
16c3i5bA_
96.8 7 PDB header:signaling protein
Chain: A: PDB Molecule:wspr response regulator;
PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa
17c3iclA_
96.7 9 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:eal/ggdef domain protein;
PDBTitle: x-ray structure of protein (eal/ggdef domain protein) from2 m.capsulatus, northeast structural genomics consortium3 target mcr174c
18c3mtkA_
96.2 9 PDB header:transferase
Chain: A: PDB Molecule:diguanylate cyclase/phosphodiesterase;
PDBTitle: x-ray structure of diguanylate cyclase/phosphodiesterase from2 caldicellulosiruptor saccharolyticus, northeast structural genomics3 consortium target clr27c
19d1w25a3
96.0 4 Fold:Ferredoxin-like
Superfamily:Nucleotide cyclase
Family:GGDEF domain
20c3ignA_
95.9 8 PDB header:transferase
Chain: A: PDB Molecule:diguanylate cyclase;
PDBTitle: crystal structure of the ggdef domain from marinobacter2 aquaeolei diguanylate cyclase complexed with c-di-gmp -3 northeast structural genomics consortium target mqr89a
21c3hvaA_
not modelled 95.7 10 PDB header:transferase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa
22c3qyyB_
not modelled 95.3 9 PDB header:signaling protein/inhibitor
Chain: B: PDB Molecule:response regulator;
PDBTitle: a novel interaction mode between a microbial ggdef domain and the bis-2 (3, 5 )-cyclic di-gmp
23c3hvwA_
not modelled 94.5 11 PDB header:lyase
Chain: A: PDB Molecule:diguanylate-cyclase (dgc);
PDBTitle: crystal structure of the ggdef domain of the pa2567 protein2 from pseudomonas aeruginosa, northeast structural genomics3 consortium target par365c
24c2p0oA_
not modelled 94.2 17 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein duf871;
PDBTitle: crystal structure of a conserved protein from locus ef_2437 in2 enterococcus faecalis with an unknown function
25d1p6qa_
not modelled 93.9 9 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
26c3khtA_
not modelled 93.4 16 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator;
PDBTitle: crystal structure of response regulator from hahella chejuensis
27c2zayA_
not modelled 93.3 14 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of response regulator from desulfuromonas2 acetoxidans
28d1mvoa_
not modelled 93.0 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
29c3hebB_
not modelled 93.0 16 PDB header:transcription regulator
Chain: B: PDB Molecule:response regulator receiver domain protein (chey);
PDBTitle: crystal structure of response regulator receiver domain from2 rhodospirillum rubrum
30c2ayxA_
not modelled 92.4 16 PDB header:transferase
Chain: A: PDB Molecule:sensor kinase protein rcsc;
PDBTitle: solution structure of the e.coli rcsc c-terminus (residues2 700-949) containing linker region and phosphoreceiver3 domain
31d1heya_
not modelled 90.9 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
32d1gjwa2
not modelled 90.9 8 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
33d1w25a1
not modelled 90.2 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
34d1ua7a2
not modelled 89.7 11 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
35d1h5ya_
not modelled 89.6 13 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Histidine biosynthesis enzymes
36c2jk1A_
not modelled 89.5 7 PDB header:dna-binding
Chain: A: PDB Molecule:hydrogenase transcriptional regulatory protein hupr1;
PDBTitle: crystal structure of the wild-type hupr receiver domain
37c3rqiA_
not modelled 89.1 15 PDB header:transcription
Chain: A: PDB Molecule:response regulator protein;
PDBTitle: crystal structure of a response regulator protein from burkholderia2 pseudomallei with a phosphorylated aspartic acid, calcium ion and3 citrate
38c2yxbA_
not modelled 89.1 13 PDB header:isomerase
Chain: A: PDB Molecule:coenzyme b12-dependent mutase;
PDBTitle: crystal structure of the methylmalonyl-coa mutase alpha-subunit from2 aeropyrum pernix
39c2c3zA_
not modelled 88.7 14 PDB header:lyase
Chain: A: PDB Molecule:indole-3-glycerol phosphate synthase;
PDBTitle: crystal structure of a truncated variant of indole-3-2 glycerol phosphate synthase from sulfolobus solfataricus
40d2ayxa1
not modelled 88.1 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
41d1krwa_
not modelled 88.0 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
42d1qkka_
not modelled 87.8 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
43c3gt7A_
not modelled 87.7 10 PDB header:hydrolase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of signal receiver domain of signal2 transduction histidine kinase from syntrophus3 aciditrophicus
44d1y0ea_
not modelled 87.7 11 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:NanE-like
45c2h6rG_
not modelled 87.4 11 PDB header:isomerase
Chain: G: PDB Molecule:triosephosphate isomerase;
PDBTitle: crystal structure of triosephosphate isomerase (tim) from2 methanocaldococcus jannaschii
46d1jbea_
not modelled 87.4 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
47d1k68a_
not modelled 87.2 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
48c3i42A_
not modelled 87.1 14 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:response regulator receiver domain protein (chey-
PDBTitle: structure of response regulator receiver domain (chey-like)2 from methylobacillus flagellatus
49c2y85D_
not modelled 86.0 21 PDB header:isomerase
Chain: D: PDB Molecule:phosphoribosyl isomerase a;
PDBTitle: crystal structure of mycobacterium tuberculosis phosphoribosyl2 isomerase with bound rcdrp
50c3eulB_
not modelled 85.9 11 PDB header:transcription
Chain: B: PDB Molecule:possible nitrate/nitrite response transcriptional
PDBTitle: structure of the signal receiver domain of the putative2 response regulator narl from mycobacterium tuberculosis
51c3gl9B_
not modelled 85.7 14 PDB header:signaling protein
Chain: B: PDB Molecule:response regulator;
PDBTitle: the structure of a histidine kinase-response regulator2 complex sheds light into two-component signaling and3 reveals a novel cis autophosphorylation mechanism
52d2pl1a1
not modelled 85.6 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
53d1zesa1
not modelled 85.6 10 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
54d1yioa2
not modelled 85.5 8 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
55c3crnA_
not modelled 85.1 13 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver domain protein, chey-like;
PDBTitle: crystal structure of response regulator receiver domain protein (chey-2 like) from methanospirillum hungatei jf-1
56d1kgsa2
not modelled 85.0 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
57c2v82A_
not modelled 85.0 19 PDB header:lyase
Chain: A: PDB Molecule:2-dehydro-3-deoxy-6-phosphogalactonate aldolase;
PDBTitle: kdpgal complexed to kdpgal
58c3q58A_
not modelled 85.0 11 PDB header:isomerase
Chain: A: PDB Molecule:n-acetylmannosamine-6-phosphate 2-epimerase;
PDBTitle: structure of n-acetylmannosamine-6-phosphate epimerase from salmonella2 enterica
59d2r25b1
not modelled 84.7 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
60d1i3ca_
not modelled 84.7 15 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
61c2pz0B_
not modelled 84.3 9 PDB header:hydrolase
Chain: B: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of glycerophosphodiester phosphodiesterase (gdpd)2 from t. tengcongensis
62d1u0sy_
not modelled 84.2 11 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
63c2j48A_
not modelled 84.1 17 PDB header:transferase
Chain: A: PDB Molecule:two-component sensor kinase;
PDBTitle: nmr structure of the pseudo-receiver domain of the cika2 protein.
64c3hv2B_
not modelled 83.7 14 PDB header:signaling protein
Chain: B: PDB Molecule:response regulator/hd domain protein;
PDBTitle: crystal structure of signal receiver domain of hd domain-2 containing protein from pseudomonas fluorescens pf-5
65c3nhzA_
not modelled 83.3 12 PDB header:dna binding protein
Chain: A: PDB Molecule:two component system transcriptional regulator mtra;
PDBTitle: structure of n-terminal domain of mtra
66d1ys7a2
not modelled 83.2 14 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
67d2d3na2
not modelled 82.9 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
68c1jibA_
not modelled 82.8 23 PDB header:hydrolase
Chain: A: PDB Molecule:neopullulanase;
PDBTitle: complex of alpha-amylase ii (tva ii) from thermoactinomyces2 vulgaris r-47 with maltotetraose based on a crystal soaked3 with maltohexaose.
69d1ny5a1
not modelled 82.5 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
70c3gr7A_
not modelled 82.5 9 PDB header:oxidoreductase
Chain: A: PDB Molecule:nadph dehydrogenase;
PDBTitle: structure of oye from geobacillus kaustophilus, hexagonal2 crystal form
71d1dz3a_
not modelled 82.3 17 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
72d1hvxa2
not modelled 82.3 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
73c3b2nA_
not modelled 81.4 10 PDB header:transcription
Chain: A: PDB Molecule:uncharacterized protein q99uf4;
PDBTitle: crystal structure of dna-binding response regulator, luxr family, from2 staphylococcus aureus
74c3cg0A_
not modelled 81.3 13 PDB header:lyase
Chain: A: PDB Molecule:response regulator receiver modulated diguanylate cyclase
PDBTitle: crystal structure of signal receiver domain of modulated diguanylate2 cyclase from desulfovibrio desulfuricans g20, an example of alternate3 folding
75c3c3mA_
not modelled 80.8 10 PDB header:signaling protein
Chain: A: PDB Molecule:response regulator receiver protein;
PDBTitle: crystal structure of the n-terminal domain of response regulator2 receiver protein from methanoculleus marisnigri jr1
76d1uoka2
not modelled 80.5 19 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
77c3a23A_
not modelled 80.4 14 PDB header:hydrolase
Chain: A: PDB Molecule:putative secreted alpha-galactosidase;
PDBTitle: crystal structure of beta-l-arabinopyranosidase complexed with d-2 galactose
78c3c97A_
not modelled 80.4 10 PDB header:signaling protein, transferase
Chain: A: PDB Molecule:signal transduction histidine kinase;
PDBTitle: crystal structure of the response regulator receiver domain2 of a signal transduction histidine kinase from aspergillus3 oryzae
79d2guya2
not modelled 80.3 9 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
80c1qhoA_
not modelled 80.3 24 PDB header:hydrolase
Chain: A: PDB Molecule:alpha-amylase;
PDBTitle: five-domain alpha-amylase from bacillus stearothermophilus,2 maltose/acarbose complex
81d1dbwa_
not modelled 80.2 13 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
82d2gjpa2
not modelled 80.0 12 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
83c3cnbC_
not modelled 79.7 16 PDB header:dna binding protein
Chain: C: PDB Molecule:dna-binding response regulator, merr family;
PDBTitle: crystal structure of signal receiver domain of dna binding response2 regulator protein (merr) from colwellia psychrerythraea 34h
84d1k66a_
not modelled 79.5 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
85c1gjuA_
not modelled 79.2 8 PDB header:transferase
Chain: A: PDB Molecule:maltodextrin glycosyltransferase;
PDBTitle: maltosyltransferase from thermotoga maritima
86d1ob0a2
not modelled 79.1 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
87d1mxga2
not modelled 79.1 8 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
88d1xhfa1
not modelled 79.0 8 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
89d2p10a1
not modelled 79.0 25 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Mll9387-like
90d1ud2a2
not modelled 78.9 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
91d1h3ga3
not modelled 78.8 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
92d1ea9c3
not modelled 78.4 17 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
93c1yadD_
not modelled 78.2 18 PDB header:transcription
Chain: D: PDB Molecule:regulatory protein teni;
PDBTitle: structure of teni from bacillus subtilis
94c1cygA_
not modelled 78.1 17 PDB header:glycosyltransferase
Chain: A: PDB Molecule:cyclodextrin glucanotransferase;
PDBTitle: cyclodextrin glucanotransferase (e.c.2.4.1.19) (cgtase)
95d1lwha2
not modelled 78.0 16 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
96c1ea9D_
not modelled 77.8 18 PDB header:hydrolase
Chain: D: PDB Molecule:cyclomaltodextrinase;
PDBTitle: cyclomaltodextrinase
97d1g5aa2
not modelled 77.8 16 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
98d1rd5a_
not modelled 77.7 12 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
99d1cgta4
not modelled 77.5 17 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
100c2zwmA_
not modelled 77.4 12 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulatory protein yycf;
PDBTitle: crystal structure of yycf receiver domain from bacillus2 subtilis
101c3grcD_
not modelled 77.4 9 PDB header:transferase
Chain: D: PDB Molecule:sensor protein, kinase;
PDBTitle: crystal structure of a sensor protein from polaromonas sp.2 js666
102c2rjnA_
not modelled 77.2 10 PDB header:hydrolase
Chain: A: PDB Molecule:response regulator receiver:metal-dependent
PDBTitle: crystal structure of an uncharacterized protein q2bku2 from2 neptuniibacter caesariensis
103c3lteH_
not modelled 77.2 13 PDB header:transcription
Chain: H: PDB Molecule:response regulator;
PDBTitle: crystal structure of response regulator (signal receiver domain) from2 bermanella marisrubri
104c3hdgE_
not modelled 76.8 16 PDB header:structural genomics, unknown function
Chain: E: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of the n-terminal domain of an2 uncharacterized protein (ws1339) from wolinella3 succinogenes
105c1ud8A_
not modelled 76.8 10 PDB header:hydrolase
Chain: A: PDB Molecule:amylase;
PDBTitle: crystal structure of amyk38 with lithium ion
106d1e43a2
not modelled 76.7 10 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
107d2aaaa2
not modelled 76.5 12 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
108c3kruC_
not modelled 76.2 16 PDB header:oxidoreductase
Chain: C: PDB Molecule:nadh:flavin oxidoreductase/nadh oxidase;
PDBTitle: crystal structure of the thermostable old yellow enzyme from2 thermoanaerobacter pseudethanolicus e39
109c1uasA_
not modelled 76.2 24 PDB header:hydrolase
Chain: A: PDB Molecule:alpha-galactosidase;
PDBTitle: crystal structure of rice alpha-galactosidase
110c2aaaA_
not modelled 75.8 12 PDB header:glycosidase
Chain: A: PDB Molecule:alpha-amylase;
PDBTitle: calcium binding in alpha-amylases: an x-ray diffraction2 study at 2.1 angstroms resolution of two enzymes from3 aspergillus
111d1pama4
not modelled 75.7 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
112c3bmwA_
not modelled 75.6 22 PDB header:transferase
Chain: A: PDB Molecule:cyclomaltodextrin glucanotransferase;
PDBTitle: cyclodextrin glycosyl transferase from thermoanerobacterium2 thermosulfurigenes em1 mutant s77p complexed with a maltoheptaose3 inhibitor
113c2jrlA_
not modelled 75.3 13 PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator (ntrc family);
PDBTitle: solution structure of the beryllofluoride-activated ntrc4 receiver2 domain dimer
114c1jgiA_
not modelled 75.0 15 PDB header:transferase
Chain: A: PDB Molecule:amylosucrase;
PDBTitle: crystal structure of the active site mutant glu328gln of2 amylosucrase from neisseria polysaccharea in complex with3 the natural substrate sucrose
115c3cg4A_
not modelled 75.0 11 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:response regulator receiver domain protein (chey-like);
PDBTitle: crystal structure of response regulator receiver domain protein (chey-2 like) from methanospirillum hungatei jf-1
116c3cu5B_
not modelled 74.9 14 PDB header:transcription regulator
Chain: B: PDB Molecule:two component transcriptional regulator, arac family;
PDBTitle: crystal structure of a two component transcriptional regulator arac2 from clostridium phytofermentans isdg
117d1gvia3
not modelled 74.8 20 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
118c3igsB_
not modelled 74.5 11 PDB header:isomerase
Chain: B: PDB Molecule:n-acetylmannosamine-6-phosphate 2-epimerase 2;
PDBTitle: structure of the salmonella enterica n-acetylmannosamine-6-phosphate2 2-epimerase
119d1a04a2
not modelled 74.3 16 Fold:Flavodoxin-like
Superfamily:CheY-like
Family:CheY-related
120c3ffsC_
not modelled 74.1 13 PDB header:oxidoreductase
Chain: C: PDB Molecule:inosine-5-monophosphate dehydrogenase;
PDBTitle: the crystal structure of cryptosporidium parvum inosine-5'-2 monophosphate dehydrogenase

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