Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP09394
DateThu Jan 5 11:02:21 GMT 2012
Unique Job IDffdbd3855c0a7676

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template c1ydyA_
Top template information
PDB header:hydrolase
Chain: A: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of periplasmic glycerophosphodiester2 phosphodiesterase from escherichia coli
Confidence and coverage
Confidence:100.0% Coverage: 92%
328 residues ( 92% 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  MKLTLKNLSMAIMMSTIVMGSSAMAADSNEKIVIAHRGASGYLPEHTLPAKAMAYAQGAD
Secondary structure 
SS confidence 
Disorder  ???
????????????
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  YLEQDLVMTKDDNLVVLHDHYLDRVTDVADRFPDRARKDGRYYAIDFTLDEIKSLKFTEG
Secondary structure 
SS confidence 
Disorder 
????
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  FDIENGKKVQTYPGRFPMGKSDFRVHTFEEEIEFVQGLNHSTGKNIGIYPEIKAPWFHHQ
Secondary structure 
SS confidence 
Disorder 
????
?
?
??
????
???
Disorder confidence 
 
   .........190.........200.........210.........220.........230.........240
Sequence  EGKDIAAKTLEVLKKYGYTGKDDKVYLQCFDADELKRIKNELEPKMGMELNLVQLIAYTD
Secondary structure 
SS confidence 
Disorder 
?
Disorder confidence 
 
   .........250.........260.........270.........280.........290.........300
Sequence  WNETQQKQPDGSWVNYNYDWMFKPGAMKQVAEYADGIGPDYHMLIEETSQPGNIKLTGMV
Secondary structure 
SS confidence 
Disorder  ??????????
??
?????
Disorder confidence 
 
   .........310.........320.........330.........340.........350........
Sequence  QDAQQNKLVVHPYTVRSDKLPEYTPDVNQLYDALYNKAGVNGLFTDFPDKAVKFLNKE
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 1ydy chain A

3D model

Region: 29 - 356
Aligned: 328
Modelled: 328
Confidence: 100.0%
Identity: 100%
PDB header:hydrolase
Chain: A: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of periplasmic glycerophosphodiester2 phosphodiesterase from escherichia coli

Phyre2

PDB 1ydy chain A domain 1

3D model

Region: 29 - 356
Aligned: 328
Modelled: 328
Confidence: 100.0%
Identity: 100%
Fold: TIM beta/alpha-barrel
Superfamily: PLC-like phosphodiesterases
Family: Glycerophosphoryl diester phosphodiesterase

Phyre2

PDB 3l12 chain A

3D model

Region: 25 - 358
Aligned: 284
Modelled: 299
Confidence: 100.0%
Identity: 20%
PDB header:hydrolase
Chain: A: PDB Molecule:putative glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of putative glycerophosphoryl diester2 phosphodiesterase (yp_165505.1) from silicibacter pomeroyi dss-3 at3 1.60 a resolution

Phyre2

PDB 2p76 chain H

3D model

Region: 27 - 357
Aligned: 260
Modelled: 308
Confidence: 100.0%
Identity: 33%
PDB header:hydrolase
Chain: H: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of a glycerophosphodiester phosphodiesterase from2 staphylococcus aureus

Phyre2

PDB 2pz0 chain B

3D model

Region: 30 - 358
Aligned: 241
Modelled: 264
Confidence: 100.0%
Identity: 32%
PDB header:hydrolase
Chain: B: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of glycerophosphodiester phosphodiesterase (gdpd)2 from t. tengcongensis

Phyre2

PDB 3mz2 chain A

3D model

Region: 26 - 357
Aligned: 250
Modelled: 259
Confidence: 100.0%
Identity: 18%
PDB header:hydrolase
Chain: A: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of a glycerophosphoryl diester phosphodiesterase2 (bdi_3922) from parabacteroides distasonis atcc 8503 at 1.55 a3 resolution

Phyre2

PDB 3qvq chain B

3D model

Region: 31 - 357
Aligned: 240
Modelled: 279
Confidence: 100.0%
Identity: 26%
PDB header:hydrolase
Chain: B: PDB Molecule:phosphodiesterase olei02445;
PDBTitle: the structure of an oleispira antarctica phosphodiesterase olei024452 in complex with the product sn-glycerol-3-phosphate

Phyre2

PDB 2otd chain C

3D model

Region: 26 - 355
Aligned: 243
Modelled: 270
Confidence: 100.0%
Identity: 19%
PDB header:hydrolase
Chain: C: PDB Molecule:glycerophosphodiester phosphodiesterase;
PDBTitle: the crystal structure of the glycerophosphodiester phosphodiesterase2 from shigella flexneri 2a

Phyre2

PDB 1zcc chain A domain 1

3D model

Region: 31 - 357
Aligned: 233
Modelled: 260
Confidence: 100.0%
Identity: 26%
Fold: TIM beta/alpha-barrel
Superfamily: PLC-like phosphodiesterases
Family: Glycerophosphoryl diester phosphodiesterase

Phyre2

PDB 3ch0 chain A

3D model

Region: 27 - 353
Aligned: 265
Modelled: 281
Confidence: 100.0%
Identity: 24%
PDB header:hydrolase
Chain: A: PDB Molecule:glycerophosphodiester phosphodiesterase;
PDBTitle: crystal structure of glycerophosphoryl diester phosphodiesterase2 (yp_677622.1) from cytophaga hutchinsonii atcc 33406 at 1.50 a3 resolution

Phyre2

PDB 3no3 chain A

3D model

Region: 28 - 358
Aligned: 233
Modelled: 246
Confidence: 100.0%
Identity: 24%
PDB header:hydrolase
Chain: A: PDB Molecule:glycerophosphodiester phosphodiesterase;
PDBTitle: crystal structure of a glycerophosphodiester phosphodiesterase2 (bdi_0402) from parabacteroides distasonis atcc 8503 at 1.89 a3 resolution

Phyre2

PDB 3ks6 chain A

3D model

Region: 30 - 357
Aligned: 242
Modelled: 290
Confidence: 100.0%
Identity: 22%
PDB header:hydrolase
Chain: A: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of putative glycerophosphoryl diester2 phosphodiesterase (17743486) from agrobacterium tumefaciens3 str. c58 (dupont) at 1.80 a resolution

Phyre2

PDB 1vd6 chain A domain 1

3D model

Region: 31 - 356
Aligned: 217
Modelled: 236
Confidence: 100.0%
Identity: 21%
Fold: TIM beta/alpha-barrel
Superfamily: PLC-like phosphodiesterases
Family: Glycerophosphoryl diester phosphodiesterase

Phyre2

PDB 3i10 chain A

3D model

Region: 26 - 358
Aligned: 257
Modelled: 279
Confidence: 100.0%
Identity: 25%
PDB header:hydrolase
Chain: A: PDB Molecule:putative glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of putative glycerophosphoryl diester2 phosphodiesterase (np_812074.1) from bacteroides thetaiotaomicron3 vpi-5482 at 1.35 a resolution

Phyre2

PDB 2o55 chain A

3D model

Region: 31 - 356
Aligned: 239
Modelled: 275
Confidence: 100.0%
Identity: 23%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative glycerophosphodiester phosphodiesterase;
PDBTitle: crystal structure of a putative glycerophosphodiester2 phosphodiesterase from galdieria sulphuraria

Phyre2

PDB 1o1z chain A

3D model

Region: 28 - 354
Aligned: 224
Modelled: 276
Confidence: 100.0%
Identity: 27%
Fold: TIM beta/alpha-barrel
Superfamily: PLC-like phosphodiesterases
Family: Glycerophosphoryl diester phosphodiesterase

Phyre2

PDB 3rlh chain A

3D model

Region: 28 - 358
Aligned: 246
Modelled: 281
Confidence: 100.0%
Identity: 17%
PDB header:hydrolase
Chain: A: PDB Molecule:sphingomyelin phosphodiesterase d lisictox-alphaia1a;
PDBTitle: crystal structure of a class ii phospholipase d from loxosceles2 intermedia venom

Phyre2

PDB 3rlg chain A

3D model

Region: 28 - 358
Aligned: 253
Modelled: 271
Confidence: 100.0%
Identity: 17%
PDB header:hydrolase
Chain: A: PDB Molecule:sphingomyelin phosphodiesterase d lisictox-alphaia1a;
PDBTitle: crystal structure of loxosceles intermedia phospholipase d isoform 12 h12a mutant

Phyre2

PDB 2f9r chain C

3D model

Region: 26 - 358
Aligned: 247
Modelled: 270
Confidence: 100.0%
Identity: 16%
PDB header:hydrolase
Chain: C: PDB Molecule:sphingomyelinase d 1;
PDBTitle: crystal structure of the inactive state of the smase i, a2 sphingomyelinase d from loxosceles laeta venom

Phyre2

PDB 1djy chain B

3D model

Region: 45 - 196
Aligned: 85
Modelled: 92
Confidence: 98.0%
Identity: 16%
PDB header:lipid degradation
Chain: B: PDB Molecule:phosphoinositide-specific phospholipase c,
PDBTitle: phosphoinositide-specific phospholipase c-delta1 from rat2 complexed with inositol-2,4,5-trisphosphate

Phyre2

PDB 3nvt chain A

3D model

Region: 14 - 71
Aligned: 58
Modelled: 58
Confidence: 80.4%
Identity: 24%
PDB header:transferase/isomerase
Chain: A: PDB Molecule:3-deoxy-d-arabino-heptulosonate 7-phosphate synthase;
PDBTitle: 1.95 angstrom crystal structure of a bifunctional 3-deoxy-7-2 phosphoheptulonate synthase/chorismate mutase (aroa) from listeria3 monocytogenes egd-e

Phyre2
1
c1ydyA_
2
d1ydya1
3
c3l12A_
4
c2p76H_
5
c2pz0B_
6
c3mz2A_
7
c3qvqB_
8
c2otdC_
9
d1zcca1
10
c3ch0A_
11
c3no3A_
12
c3ks6A_
13
d1vd6a1
14
c3i10A_
15
c2o55A_
16
d1o1za_
17
c3rlhA_
18
c3rlgA_
19
c2f9rC_
20
c1djyB_
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
c3nvtA_
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



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c1ydyA_
100.0 100 PDB header:hydrolase
Chain: A: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of periplasmic glycerophosphodiester2 phosphodiesterase from escherichia coli
2d1ydya1
100.0 100 Fold:TIM beta/alpha-barrel
Superfamily:PLC-like phosphodiesterases
Family:Glycerophosphoryl diester phosphodiesterase
3c3l12A_
100.0 20 PDB header:hydrolase
Chain: A: PDB Molecule:putative glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of putative glycerophosphoryl diester2 phosphodiesterase (yp_165505.1) from silicibacter pomeroyi dss-3 at3 1.60 a resolution
4c2p76H_
100.0 33 PDB header:hydrolase
Chain: H: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of a glycerophosphodiester phosphodiesterase from2 staphylococcus aureus
5c2pz0B_
100.0 32 PDB header:hydrolase
Chain: B: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of glycerophosphodiester phosphodiesterase (gdpd)2 from t. tengcongensis
6c3mz2A_
100.0 18 PDB header:hydrolase
Chain: A: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of a glycerophosphoryl diester phosphodiesterase2 (bdi_3922) from parabacteroides distasonis atcc 8503 at 1.55 a3 resolution
7c3qvqB_
100.0 26 PDB header:hydrolase
Chain: B: PDB Molecule:phosphodiesterase olei02445;
PDBTitle: the structure of an oleispira antarctica phosphodiesterase olei024452 in complex with the product sn-glycerol-3-phosphate
8c2otdC_
100.0 19 PDB header:hydrolase
Chain: C: PDB Molecule:glycerophosphodiester phosphodiesterase;
PDBTitle: the crystal structure of the glycerophosphodiester phosphodiesterase2 from shigella flexneri 2a
9d1zcca1
100.0 26 Fold:TIM beta/alpha-barrel
Superfamily:PLC-like phosphodiesterases
Family:Glycerophosphoryl diester phosphodiesterase
10c3ch0A_
100.0 24 PDB header:hydrolase
Chain: A: PDB Molecule:glycerophosphodiester phosphodiesterase;
PDBTitle: crystal structure of glycerophosphoryl diester phosphodiesterase2 (yp_677622.1) from cytophaga hutchinsonii atcc 33406 at 1.50 a3 resolution
11c3no3A_
100.0 24 PDB header:hydrolase
Chain: A: PDB Molecule:glycerophosphodiester phosphodiesterase;
PDBTitle: crystal structure of a glycerophosphodiester phosphodiesterase2 (bdi_0402) from parabacteroides distasonis atcc 8503 at 1.89 a3 resolution
12c3ks6A_
100.0 22 PDB header:hydrolase
Chain: A: PDB Molecule:glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of putative glycerophosphoryl diester2 phosphodiesterase (17743486) from agrobacterium tumefaciens3 str. c58 (dupont) at 1.80 a resolution
13d1vd6a1
100.0 21 Fold:TIM beta/alpha-barrel
Superfamily:PLC-like phosphodiesterases
Family:Glycerophosphoryl diester phosphodiesterase
14c3i10A_
100.0 25 PDB header:hydrolase
Chain: A: PDB Molecule:putative glycerophosphoryl diester phosphodiesterase;
PDBTitle: crystal structure of putative glycerophosphoryl diester2 phosphodiesterase (np_812074.1) from bacteroides thetaiotaomicron3 vpi-5482 at 1.35 a resolution
15c2o55A_
100.0 23 PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative glycerophosphodiester phosphodiesterase;
PDBTitle: crystal structure of a putative glycerophosphodiester2 phosphodiesterase from galdieria sulphuraria
16d1o1za_
100.0 27 Fold:TIM beta/alpha-barrel
Superfamily:PLC-like phosphodiesterases
Family:Glycerophosphoryl diester phosphodiesterase
17c3rlhA_
100.0 17 PDB header:hydrolase
Chain: A: PDB Molecule:sphingomyelin phosphodiesterase d lisictox-alphaia1a;
PDBTitle: crystal structure of a class ii phospholipase d from loxosceles2 intermedia venom
18c3rlgA_
100.0 17 PDB header:hydrolase
Chain: A: PDB Molecule:sphingomyelin phosphodiesterase d lisictox-alphaia1a;
PDBTitle: crystal structure of loxosceles intermedia phospholipase d isoform 12 h12a mutant
19c2f9rC_
100.0 16 PDB header:hydrolase
Chain: C: PDB Molecule:sphingomyelinase d 1;
PDBTitle: crystal structure of the inactive state of the smase i, a2 sphingomyelinase d from loxosceles laeta venom
20c1djyB_
98.0 16 PDB header:lipid degradation
Chain: B: PDB Molecule:phosphoinositide-specific phospholipase c,
PDBTitle: phosphoinositide-specific phospholipase c-delta1 from rat2 complexed with inositol-2,4,5-trisphosphate
21d1qasa3
not modelled 97.9 16 Fold:TIM beta/alpha-barrel
Superfamily:PLC-like phosphodiesterases
Family:Mammalian PLC
22d2zkmx4
not modelled 97.9 23 Fold:TIM beta/alpha-barrel
Superfamily:PLC-like phosphodiesterases
Family:Mammalian PLC
23c3ohmB_
not modelled 97.8 17 PDB header:signaling protein / hydrolase
Chain: B: PDB Molecule:1-phosphatidylinositol-4,5-bisphosphate phosphodiesterase
PDBTitle: crystal structure of activated g alpha q bound to its effector2 phospholipase c beta 3
24c3qr0A_
not modelled 97.8 16 PDB header:hydrolase
Chain: A: PDB Molecule:phospholipase c-beta (plc-beta);
PDBTitle: crystal structure of s. officinalis plc21
25c2fjuB_
not modelled 97.2 13 PDB header:signaling protein,apoptosis/hydrolase
Chain: B: PDB Molecule:1-phosphatidylinositol-4,5-bisphosphate
PDBTitle: activated rac1 bound to its effector phospholipase c beta 2
26d1vkfa_
not modelled 93.7 17 Fold:TIM beta/alpha-barrel
Superfamily:GlpP-like
Family:GlpP-like
27c3ktsA_
not modelled 93.0 12 PDB header:transcriptional regulator
Chain: A: PDB Molecule:glycerol uptake operon antiterminator regulatory protein;
PDBTitle: crystal structure of glycerol uptake operon antiterminator regulatory2 protein from listeria monocytogenes str. 4b f2365
28c2zq0B_
not modelled 92.6 6 PDB header:hydrolase
Chain: B: PDB Molecule:alpha-glucosidase (alpha-glucosidase susb);
PDBTitle: crystal structure of susb complexed with acarbose
29d2gjpa2
not modelled 92.3 10 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
30d1ob0a2
not modelled 90.3 12 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
31c3a24A_
not modelled 89.4 17 PDB header:hydrolase
Chain: A: PDB Molecule:alpha-galactosidase;
PDBTitle: crystal structure of bt1871 retaining glycosidase
32d1pkla2
not modelled 88.8 13 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
33c1mwoA_
not modelled 88.6 13 PDB header:hydrolase
Chain: A: PDB Molecule:alpha amylase;
PDBTitle: crystal structure analysis of the hyperthermostable2 pyrocoocus woesei alpha-amylase
34d1e43a2
not modelled 87.0 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
35c2qpuB_
not modelled 85.1 10 PDB header:hydrolase
Chain: B: PDB Molecule:alpha-amylase type a isozyme;
PDBTitle: sugar tongs mutant s378p in complex with acarbose
36d1e0ta2
not modelled 83.2 22 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
37c1bplA_
not modelled 83.0 13 PDB header:glycosyltransferase
Chain: A: PDB Molecule:alpha-1,4-glucan-4-glucanohydrolase;
PDBTitle: glycosyltransferase
38c3h4wA_
not modelled 82.5 16 PDB header:hydrolase
Chain: A: PDB Molecule:phosphatidylinositol-specific phospholipase c1;
PDBTitle: structure of a ca+2 dependent phosphatidylinositol-specific2 phospholipase c (pi-plc) enzyme from streptomyces antibioticus
39c1gcyA_
not modelled 81.3 12 PDB header:hydrolase
Chain: A: PDB Molecule:glucan 1,4-alpha-maltotetrahydrolase;
PDBTitle: high resolution crystal structure of maltotetraose-forming2 exo-amylase
40c3nvtA_
80.4 24 PDB header:transferase/isomerase
Chain: A: PDB Molecule:3-deoxy-d-arabino-heptulosonate 7-phosphate synthase;
PDBTitle: 1.95 angstrom crystal structure of a bifunctional 3-deoxy-7-2 phosphoheptulonate synthase/chorismate mutase (aroa) from listeria3 monocytogenes egd-e
41c3hvbB_
not modelled 79.3 14 PDB header:hydrolase
Chain: B: PDB Molecule:protein fimx;
PDBTitle: crystal structure of the dual-domain ggdef-eal module of2 fimx from pseudomonas aeruginosa
42c2r6oB_
not modelled 78.7 12 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
43c1jdaA_
not modelled 78.6 9 PDB header:hydrolase
Chain: A: PDB Molecule:1,4-alpha maltotetrahydrolase;
PDBTitle: maltotetraose-forming exo-amylase
44d1mxga2
not modelled 77.9 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
45d1ht6a2
not modelled 77.7 10 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
46c3thaB_
not modelled 77.0 11 PDB header:lyase
Chain: B: PDB Molecule:tryptophan synthase alpha chain;
PDBTitle: tryptophan synthase subunit alpha from campylobacter jejuni.
47c3uk2B_
not modelled 76.5 17 PDB header:ligase
Chain: B: PDB Molecule:pantothenate synthetase;
PDBTitle: the structure of pantothenate synthetase from burkholderia2 thailandensis
48d1v8fa_
not modelled 75.3 20 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)
49d1avaa2
not modelled 75.1 12 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
50d1ud2a2
not modelled 75.0 8 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
51c1uasA_
not modelled 74.5 14 PDB header:hydrolase
Chain: A: PDB Molecule:alpha-galactosidase;
PDBTitle: crystal structure of rice alpha-galactosidase
52d1gcya2
not modelled 72.6 10 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
53c3pjwA_
not modelled 72.3 16 PDB header:lyase
Chain: A: PDB Molecule:cyclic dimeric gmp binding protein;
PDBTitle: structure of pseudomonas fluorescence lapd ggdef-eal dual domain, i23
54c3khdC_
not modelled 72.1 16 PDB header:transferase
Chain: C: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure of pff1300w.
55c2ejcA_
not modelled 72.0 20 PDB header:ligase
Chain: A: PDB Molecule:pantoate--beta-alanine ligase;
PDBTitle: crystal structure of pantoate--beta-alanine ligase (panc)2 from thermotoga maritima
56c2qjhH_
not modelled 71.0 10 PDB header:lyase
Chain: H: PDB Molecule:putative aldolase mj0400;
PDBTitle: m. jannaschii adh synthase covalently bound to2 dihydroxyacetone phosphate
57c2p10D_
not modelled 70.8 26 PDB header:hydrolase
Chain: D: PDB Molecule:mll9387 protein;
PDBTitle: crystal structure of a putative phosphonopyruvate hydrolase (mll9387)2 from mesorhizobium loti maff303099 at 2.15 a resolution
58d2d3na2
not modelled 70.4 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
59c3guzB_
not modelled 67.6 19 PDB header:ligase
Chain: B: PDB Molecule:pantothenate synthetase;
PDBTitle: structural and substrate-binding studies of pantothenate2 synthenate (ps)provide insights into homotropic inhibition3 by pantoate in ps's
60d1hvxa2
not modelled 67.2 16 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
61c3hv9A_
not modelled 65.7 14 PDB header:hydrolase
Chain: A: PDB Molecule:protein fimx;
PDBTitle: crystal structure of fimx eal domain from pseudomonas aeruginosa
62d2p10a1
not modelled 65.5 24 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Mll9387-like
63c3s83A_
not modelled 65.3 22 PDB header:signaling protein
Chain: A: PDB Molecule:ggdef family protein;
PDBTitle: crystal structure of eal domain from caulobacter crescentus cb15
64d1h7na_
not modelled 64.6 15 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)
65c3n8hA_
not modelled 64.5 17 PDB header:ligase
Chain: A: PDB Molecule:pantothenate synthetase;
PDBTitle: crystal structure of pantoate-beta-alanine ligase from francisella2 tularensis
66c1aqfB_
not modelled 58.2 16 PDB header:transferase
Chain: B: PDB Molecule:pyruvate kinase;
PDBTitle: pyruvate kinase from rabbit muscle with mg, k, and l-2 phospholactate
67c2dh3A_
not modelled 57.8 24 PDB header:transport protein, signaling protein
Chain: A: PDB Molecule:4f2 cell-surface antigen heavy chain;
PDBTitle: crystal structure of human ed-4f2hc
68c1t5aB_
not modelled 54.9 20 PDB header:transferase
Chain: B: PDB Molecule:pyruvate kinase, m2 isozyme;
PDBTitle: human pyruvate kinase m2
69c3blpX_
not modelled 54.5 9 PDB header:hydrolase
Chain: X: PDB Molecule:alpha-amylase 1;
PDBTitle: role of aromatic residues in human salivary alpha-amylase
70c3gndC_
not modelled 54.3 16 PDB header:lyase
Chain: C: PDB Molecule:aldolase lsrf;
PDBTitle: crystal structure of e. coli lsrf in complex with ribulose-5-phosphate
71d1ktba2
not modelled 53.9 18 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
72c3gfzB_
not modelled 53.8 11 PDB header:hydrolase, signaling protein
Chain: B: PDB Molecule:klebsiella pneumoniae blrp1;
PDBTitle: klebsiella pneumoniae blrp1 ph 6 manganese/cy-digmp complex
73c3pfmA_
not modelled 53.5 15 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
74d1ujpa_
not modelled 53.4 26 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
75d2f06a2
not modelled 53.3 18 Fold:Ferredoxin-like
Superfamily:ACT-like
Family:BT0572-like
76c2vgbB_
not modelled 53.1 19 PDB header:transferase
Chain: B: PDB Molecule:pyruvate kinase isozymes r/l;
PDBTitle: human erythrocyte pyruvate kinase
77d1ua7a2
not modelled 52.6 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
78d1pv8a_
not modelled 51.0 15 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)
79d1jaea2
not modelled 51.0 13 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
80c2ekcA_
not modelled 50.6 23 PDB header:lyase
Chain: A: PDB Molecule:tryptophan synthase alpha chain;
PDBTitle: structural study of project id aq_1548 from aquifex aeolicus vf5
81c1pklB_
not modelled 50.2 15 PDB header:transferase
Chain: B: PDB Molecule:protein (pyruvate kinase);
PDBTitle: the structure of leishmania pyruvate kinase
82d1hx0a2
not modelled 49.5 9 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
83c3kzpA_
not modelled 48.6 23 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
84c3ma8A_
not modelled 48.3 15 PDB header:transferase
Chain: A: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure of cgd1_2040, a pyruvate kinase from cryptosporidium2 parvum
85d1ihoa_
not modelled 47.9 19 Fold:Adenine nucleotide alpha hydrolase-like
Superfamily:Nucleotidylyl transferase
Family:Pantothenate synthetase (Pantoate-beta-alanine ligase, PanC)
86c3e0vB_
not modelled 47.4 15 PDB header:transferase
Chain: B: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure of pyruvate kinase from leishmania mexicana in2 complex with sulphate ions
87d1bxba_
not modelled 47.1 14 Fold:TIM beta/alpha-barrel
Superfamily:Xylose isomerase-like
Family:Xylose isomerase
88d1rd5a_
not modelled 46.8 21 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
89c3mxtA_
not modelled 46.5 15 PDB header:ligase
Chain: A: PDB Molecule:pantothenate synthetase;
PDBTitle: crystal structure of pantoate-beta-alanine ligase from campylobacter2 jejuni
90d1r46a2
not modelled 45.0 12 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
91d1qopa_
not modelled 43.3 21 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:Tryptophan biosynthesis enzymes
92d1kjqa2
not modelled 42.4 8 Fold:PreATP-grasp domain
Superfamily:PreATP-grasp domain
Family:BC N-terminal domain-like
93c3l2iB_
not modelled 42.0 19 PDB header:lyase
Chain: B: PDB Molecule:3-dehydroquinate dehydratase;
PDBTitle: 1.85 angstrom crystal structure of the 3-dehydroquinate dehydratase2 (arod) from salmonella typhimurium lt2.
94c3navB_
not modelled 41.7 21 PDB header:lyase
Chain: B: PDB Molecule:tryptophan synthase alpha chain;
PDBTitle: crystal structure of an alpha subunit of tryptophan synthase from2 vibrio cholerae o1 biovar el tor str. n16961
95d2f6ua1
not modelled 41.3 14 Fold:TIM beta/alpha-barrel
Superfamily:FMN-linked oxidoreductases
Family:FMN-linked oxidoreductases
96d2g50a2
not modelled 41.2 16 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
97c1ud8A_
not modelled 41.1 6 PDB header:hydrolase
Chain: A: PDB Molecule:amylase;
PDBTitle: crystal structure of amyk38 with lithium ion
98d1tqxa_
not modelled 41.1 21 Fold:TIM beta/alpha-barrel
Superfamily:Ribulose-phoshate binding barrel
Family:D-ribulose-5-phosphate 3-epimerase
99d1a3xa2
not modelled 40.4 13 Fold:TIM beta/alpha-barrel
Superfamily:Phosphoenolpyruvate/pyruvate domain
Family:Pyruvate kinase
100c3t07D_
not modelled 40.4 15 PDB header:transferase/transferase inhibitor
Chain: D: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure of s. aureus pyruvate kinase in complex with a2 naturally occurring bis-indole alkaloid
101c3femB_
not modelled 40.0 24 PDB header:biosynthetic protein, transferase
Chain: B: PDB Molecule:pyridoxine biosynthesis protein snz1;
PDBTitle: structure of the synthase subunit pdx1.1 (snz1) of plp synthase from2 saccharomyces cerevisiae
102c3obkH_
not modelled 40.0 16 PDB header:lyase
Chain: H: PDB Molecule:delta-aminolevulinic acid dehydratase;
PDBTitle: crystal structure of delta-aminolevulinic acid dehydratase2 (porphobilinogen synthase) from toxoplasma gondii me49 in complex3 with the reaction product porphobilinogen
103c2nv2U_
not modelled 39.8 27 PDB header:lyase/transferase
Chain: U: PDB Molecule:pyridoxal biosynthesis lyase pdxs;
PDBTitle: structure of the plp synthase complex pdx1/2 (yaad/e) from bacillus2 subtilis
104d2ptda_
not modelled 39.2 21 Fold:TIM beta/alpha-barrel
Superfamily:PLC-like phosphodiesterases
Family:Bacterial PLC
105c3o6cA_
not modelled 39.0 13 PDB header:transferase
Chain: A: PDB Molecule:pyridoxine 5'-phosphate synthase;
PDBTitle: pyridoxal phosphate biosynthetic protein pdxj from campylobacter2 jejuni
106c2zbtB_
not modelled 38.9 20 PDB header:lyase
Chain: B: PDB Molecule:pyridoxal biosynthesis lyase pdxs;
PDBTitle: crystal structure of pyridoxine biosynthesis protein from thermus2 thermophilus hb8
107c2htmB_
not modelled 38.3 14 PDB header:biosynthetic protein
Chain: B: PDB Molecule:thiazole biosynthesis protein thig;
PDBTitle: crystal structure of ttha0676 from thermus thermophilus hb8
108c1a3wB_
not modelled 38.2 12 PDB header:transferase
Chain: B: PDB Molecule:pyruvate kinase;
PDBTitle: pyruvate kinase from saccharomyces cerevisiae complexed with fbp, pg,2 mn2+ and k+
109c2e28A_
not modelled 38.2 16 PDB header:transferase
Chain: A: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure analysis of pyruvate kinase from bacillus2 stearothermophilus
110d2basa1
not modelled 37.8 10 Fold:TIM beta/alpha-barrel
Superfamily:EAL domain-like
Family:EAL domain
111c1kjjA_
not modelled 37.7 8 PDB header:transferase
Chain: A: PDB Molecule:phosphoribosylglycinamide formyltransferase 2;
PDBTitle: crystal structure of glycniamide ribonucleotide2 transformylase in complex with mg-atp-gamma-s
112d1ojxa_
not modelled 36.4 12 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
113c1jaeA_
not modelled 36.0 13 PDB header:glycosidase
Chain: A: PDB Molecule:alpha-amylase;
PDBTitle: structure of tenebrio molitor larval alpha-amylase
114c3a5vA_
not modelled 35.0 16 PDB header:hydrolase
Chain: A: PDB Molecule:alpha-galactosidase;
PDBTitle: crystal structure of alpha-galactosidase i from mortierella vinacea
115c2w27A_
not modelled 33.7 11 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
116d3dhpa2
not modelled 33.4 8 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
117d1gzga_
not modelled 32.7 18 Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:5-aminolaevulinate dehydratase, ALAD (porphobilinogen synthase)
118c1e0tD_
not modelled 32.6 17 PDB header:phosphotransferase
Chain: D: PDB Molecule:pyruvate kinase;
PDBTitle: r292d mutant of e. coli pyruvate kinase
119d1uasa2
not modelled 32.5 14 Fold:TIM beta/alpha-barrel
Superfamily:(Trans)glycosidases
Family:Amylase, catalytic domain
120c3eoeC_
not modelled 32.4 15 PDB header:transferase
Chain: C: PDB Molecule:pyruvate kinase;
PDBTitle: crystal structure of pyruvate kinase from toxoplasma gondii, 55.m00007

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