Phyre 2 Results for P06983

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Email | l.a.kelley@imperial.ac.uk
Description | P06983
Date | Wed Jan 25 15:20:12 GMT 2012
Unique Job ID | e0ec6181d2febf38

Summary |

Top model
Image coloured by rainbow N → C terminus
| Close Jmol

Model (left) based on template c2ypnA_
Top template information
PDB header:transferase Chain: A: PDB Molecule:protein (hydroxymethylbilane synthase); PDBTitle: hydroxymethylbilane synthase
Confidence and coverage
Confidence: | 100.0% | Coverage: | 94%
294 residues ( 94% 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 |  | M | L | D | N | V | L | R | I | A | T | R | Q | S | P | L | A | L | W | Q | A | H | Y | V | K | D | K | L | M | A | S | H | P | G | L | V | V | E | L | V | P | M | V | T | R | G | D | V | I | L | D | T | P | L | A | K | V | G | G | K | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? |  | ? |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | L | F | V | K | E | L | E | V | A | L | L | E | N | R | A | D | I | A | V | H | S | M | K | D | V | P | V | E | F | P | Q | G | L | G | L | V | T | I | C | E | R | E | D | P | R | D | A | F | V | S | N | N | Y | D | S | L | D | A | L | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | A | G | S | I | V | G | T | S | S | L | R | R | Q | C | Q | L | A | E | R | R | P | D | L | I | I | R | S | L | R | G | N | V | G | T | R | L | S | K | L | D | N | G | E | Y | D | A | I | I | L | A | V | A | G | L | K | R | L | G | L | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | S | R | I | R | A | A | L | P | P | E | I | S | L | P | A | V | G | Q | G | A | V | G | I | E | C | R | L | D | D | S | R | T | R | E | L | L | A | A | L | N | H | H | E | T | A | L | R | V | T | A | E | R | A | M | N | T | R | L | E | G
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | G | C | Q | V | P | I | G | S | Y | A | E | L | I | D | G | E | I | W | L | R | A | L | V | G | A | P | D | G | S | Q | I | I | R | G | E | R | R | G | A | P | Q | D | A | E | Q | M | G | I | S | L | A | E | E | L | L | N | N | G | A | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | .
Sequence |  | E | I | L | A | E | V | Y | N | G | D | A | P | A
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

Rank | Aligned region
--- | ---
1 |
| c2ypnA_ |

### PDB 2ypn chain A

Region: 3 - 313
Aligned: 294
Modelled: 294
Confidence: 100.0%
Identity: 100%
PDB header:transferase
Chain: A: PDB Molecule:protein (hydroxymethylbilane synthase);
PDBTitle: hydroxymethylbilane synthase

Phyre2
2 |
| c3eq1A_ |

### PDB 3eq1 chain A

Region: 4 - 308
Aligned: 284
Modelled: 284
Confidence: 100.0%
Identity: 46%
PDB header:transferase
Chain: A: PDB Molecule:porphobilinogen deaminase;
PDBTitle: the crystal structure of human porphobilinogen deaminase at2 2.8a resolution

Phyre2
3 |
| d1pdaa1 |

### PDB 1pda chain A domain 1

Region: 3 - 219
Aligned: 208
Modelled: 217
Confidence: 100.0%
Identity: 100%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2
4 |
| d1gtka2 |

### PDB 1gtk chain A domain 2

Region: 220 - 313
Aligned: 94
Modelled: 94
Confidence: 99.9%
Identity: 100%
Fold: dsRBD-like
Superfamily: Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain
Family: Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain

Phyre2
5 |
| d1pdaa2 |

### PDB 1pda chain A domain 2

Region: 220 - 307
Aligned: 88
Modelled: 88
Confidence: 99.9%
Identity: 98%
Fold: dsRBD-like
Superfamily: Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain
Family: Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain

Phyre2
6 |
| c3gxaA_ |

### PDB 3gxa chain A

Region: 4 - 229
Aligned: 198
Modelled: 207
Confidence: 97.7%
Identity: 17%
PDB header:protein binding
Chain: A: PDB Molecule:outer membrane lipoprotein gna1946;
PDBTitle: crystal structure of gna1946

Phyre2
7 |
| c2x26A_ |

### PDB 2x26 chain A

Region: 3 - 234
Aligned: 210
Modelled: 213
Confidence: 97.7%
Identity: 16%
PDB header:transport protein
Chain: A: PDB Molecule:periplasmic aliphatic sulphonates-binding protein;
PDBTitle: crystal structure of the periplasmic aliphatic sulphonate2 binding protein ssua from escherichia coli

Phyre2
8 |
| d1p99a_ |

### PDB 1p99 chain A

Region: 5 - 231
Aligned: 197
Modelled: 208
Confidence: 97.7%
Identity: 14%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2
9 |
| c1p99A_ |

### PDB 1p99 chain A

Region: 5 - 231
Aligned: 197
Modelled: 208
Confidence: 97.7%
Identity: 14%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:hypothetical protein pg110;
PDBTitle: 1.7a crystal structure of protein pg110 from staphylococcus2 aureus

Phyre2
10 |
| c3tqwA_ |

### PDB 3tqw chain A

Region: 5 - 229
Aligned: 199
Modelled: 201
Confidence: 97.3%
Identity: 21%
PDB header:transport protein
Chain: A: PDB Molecule:methionine-binding protein;
PDBTitle: structure of a abc transporter, periplasmic substrate-binding protein2 from coxiella burnetii

Phyre2
11 |
| c3uifA_ |

### PDB 3uif chain A

Region: 4 - 238
Aligned: 212
Modelled: 217
Confidence: 97.2%
Identity: 17%
PDB header:transport protein
Chain: A: PDB Molecule:sulfonate abc transporter, periplasmic sulfonate-binding
PDBTitle: crystal structure of putative sulfonate abc transporter, periplasmic2 sulfonate-binding protein ssua from methylobacillus flagellatus kt

Phyre2
12 |
| c3ir1F_ |

### PDB 3ir1 chain F

Region: 4 - 229
Aligned: 195
Modelled: 206
Confidence: 97.1%
Identity: 18%
PDB header:protein binding
Chain: F: PDB Molecule:outer membrane lipoprotein gna1946;
PDBTitle: crystal structure of lipoprotein gna1946 from neisseria2 meningitidis

Phyre2
13 |
| c3un6A_ |

### PDB 3un6 chain A

Region: 3 - 203
Aligned: 177
Modelled: 180
Confidence: 97.1%
Identity: 15%
PDB header:unknown function
Chain: A: PDB Molecule:hypothetical protein saouhsc_00137;
PDBTitle: 2.0 angstrom crystal structure of ligand binding component of abc-type2 import system from staphylococcus aureus with zinc bound

Phyre2
14 |
| d1xs5a_ |

### PDB 1xs5 chain A

Region: 3 - 225
Aligned: 196
Modelled: 204
Confidence: 97.1%
Identity: 16%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2
15 |
| c3e4rA_ |

### PDB 3e4r chain A

Region: 3 - 234
Aligned: 209
Modelled: 213
Confidence: 96.3%
Identity: 17%
PDB header:transport protein
Chain: A: PDB Molecule:nitrate transport protein;
PDBTitle: crystal structure of the alkanesulfonate binding protein2 (ssua) from the phytopathogenic bacteria xanthomonas3 axonopodis pv. citri bound to hepes

Phyre2
16 |
| c3k2dA_ |

### PDB 3k2d chain A

Region: 3 - 229
Aligned: 193
Modelled: 209
Confidence: 95.7%
Identity: 15%
PDB header:immune system
Chain: A: PDB Molecule:abc-type metal ion transport system, periplasmic component;
PDBTitle: crystal structure of immunogenic lipoprotein a from vibrio vulnificus

Phyre2
17 |
| c3l6gA_ |

### PDB 3l6g chain A

Region: 3 - 169
Aligned: 145
Modelled: 148
Confidence: 95.6%
Identity: 12%
PDB header:glycine betaine-binding protein
Chain: A: PDB Molecule:betaine abc transporter permease and substrate binding
PDBTitle: crystal structure of lactococcal opuac in its open conformation

Phyre2
18 |
| c3qslA_ |

### PDB 3qsl chain A

Region: 1 - 171
Aligned: 149
Modelled: 152
Confidence: 95.5%
Identity: 18%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:putative exported protein;
PDBTitle: structure of cae31940 from bordetella bronchiseptica rb50

Phyre2
19 |
| c3hn0A_ |

### PDB 3hn0 chain A

Region: 3 - 171
Aligned: 139
Modelled: 140
Confidence: 95.2%
Identity: 15%
PDB header:transport protein
Chain: A: PDB Molecule:nitrate transport protein;
PDBTitle: crystal structure of an abc transporter (bdi_1369) from2 parabacteroides distasonis at 1.75 a resolution

Phyre2
20 |
| c3tmgA_ |

### PDB 3tmg chain A

Region: 4 - 234
Aligned: 203
Modelled: 212
Confidence: 93.0%
Identity: 12%
PDB header:transport protein
Chain: A: PDB Molecule:glycine betaine, l-proline abc transporter,
PDBTitle: crystal structure of glycine betaine, l-proline abc transporter,2 glycine/betaine/l-proline-binding protein (prox) from borrelia3 burgdorferi

Phyre2
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99 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2ypnA_ |
|  | 100.0 | 100 | PDB header:transferase Chain: A: PDB Molecule:protein (hydroxymethylbilane synthase); PDBTitle: hydroxymethylbilane synthase
2 | c3eq1A_ |
|  | 100.0 | 46 | PDB header:transferase Chain: A: PDB Molecule:porphobilinogen deaminase; PDBTitle: the crystal structure of human porphobilinogen deaminase at2 2.8a resolution
3 | d1pdaa1 |
|  | 100.0 | 100 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
4 | d1gtka2 |
|  | 99.9 | 100 | Fold:dsRBD-like Superfamily:Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain Family:Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain
5 | d1pdaa2 |
|  | 99.9 | 98 | Fold:dsRBD-like Superfamily:Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain Family:Porphobilinogen deaminase (hydroxymethylbilane synthase), C-terminal domain
6 | c3gxaA_ |
|  | 97.7 | 17 | PDB header:protein binding Chain: A: PDB Molecule:outer membrane lipoprotein gna1946; PDBTitle: crystal structure of gna1946
7 | c2x26A_ |
|  | 97.7 | 16 | PDB header:transport protein Chain: A: PDB Molecule:periplasmic aliphatic sulphonates-binding protein; PDBTitle: crystal structure of the periplasmic aliphatic sulphonate2 binding protein ssua from escherichia coli
8 | d1p99a_ |
|  | 97.7 | 14 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
9 | c1p99A_ |
|  | 97.7 | 14 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pg110; PDBTitle: 1.7a crystal structure of protein pg110 from staphylococcus2 aureus
10 | c3tqwA_ |
|  | 97.3 | 21 | PDB header:transport protein Chain: A: PDB Molecule:methionine-binding protein; PDBTitle: structure of a abc transporter, periplasmic substrate-binding protein2 from coxiella burnetii
11 | c3uifA_ |
|  | 97.2 | 17 | PDB header:transport protein Chain: A: PDB Molecule:sulfonate abc transporter, periplasmic sulfonate-binding PDBTitle: crystal structure of putative sulfonate abc transporter, periplasmic2 sulfonate-binding protein ssua from methylobacillus flagellatus kt
12 | c3ir1F_ |
|  | 97.1 | 18 | PDB header:protein binding Chain: F: PDB Molecule:outer membrane lipoprotein gna1946; PDBTitle: crystal structure of lipoprotein gna1946 from neisseria2 meningitidis
13 | c3un6A_ |
|  | 97.1 | 15 | PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein saouhsc_00137; PDBTitle: 2.0 angstrom crystal structure of ligand binding component of abc-type2 import system from staphylococcus aureus with zinc bound
14 | d1xs5a_ |
|  | 97.1 | 16 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
15 | c3e4rA_ |
|  | 96.3 | 17 | PDB header:transport protein Chain: A: PDB Molecule:nitrate transport protein; PDBTitle: crystal structure of the alkanesulfonate binding protein2 (ssua) from the phytopathogenic bacteria xanthomonas3 axonopodis pv. citri bound to hepes
16 | c3k2dA_ |
|  | 95.7 | 15 | PDB header:immune system Chain: A: PDB Molecule:abc-type metal ion transport system, periplasmic component; PDBTitle: crystal structure of immunogenic lipoprotein a from vibrio vulnificus
17 | c3l6gA_ |
|  | 95.6 | 12 | PDB header:glycine betaine-binding protein Chain: A: PDB Molecule:betaine abc transporter permease and substrate binding PDBTitle: crystal structure of lactococcal opuac in its open conformation
18 | c3qslA_ |
|  | 95.5 | 18 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative exported protein; PDBTitle: structure of cae31940 from bordetella bronchiseptica rb50
19 | c3hn0A_ |
|  | 95.2 | 15 | PDB header:transport protein Chain: A: PDB Molecule:nitrate transport protein; PDBTitle: crystal structure of an abc transporter (bdi_1369) from2 parabacteroides distasonis at 1.75 a resolution
20 | c3tmgA_ |
|  | 93.0 | 12 | PDB header:transport protein Chain: A: PDB Molecule:glycine betaine, l-proline abc transporter, PDBTitle: crystal structure of glycine betaine, l-proline abc transporter,2 glycine/betaine/l-proline-binding protein (prox) from borrelia3 burgdorferi
21 | d1zbma1 |
| not modelled | 92.9 | 14 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
22 | c2h9bB_ |
| not modelled | 92.3 | 32 | PDB header:transcription Chain: B: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: crystal structure of the effector binding domain of a benm variant2 (benm r156h/t157s)
23 | c3kzgB_ |
| not modelled | 91.9 | 11 | PDB header:transport protein Chain: B: PDB Molecule:arginine 3rd transport system periplasmic binding PDBTitle: crystal structure of an arginine 3rd transport system2 periplasmic binding protein from legionella pneumophila
24 | d2czla1 |
| not modelled | 91.8 | 18 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
25 | d2ozza1 |
| not modelled | 90.9 | 19 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
26 | c2f7cA_ |
| not modelled | 90.1 | 23 | PDB header:gene regulation Chain: A: PDB Molecule:hth-type transcriptional regulator catm; PDBTitle: catm effector binding domain with its effector cis,cis-muconate
27 | c3ix1A_ |
| not modelled | 87.3 | 17 | PDB header:biosynthetic protein Chain: A: PDB Molecule:n-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding PDBTitle: periplasmic n-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding2 protein from bacillus halodurans
28 | c3ix1B_ |
| not modelled | 87.3 | 17 | PDB header:biosynthetic protein Chain: B: PDB Molecule:n-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding PDBTitle: periplasmic n-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding2 protein from bacillus halodurans
29 | c3ho7A_ |
| not modelled | 84.5 | 22 | PDB header:transcription Chain: A: PDB Molecule:oxyr; PDBTitle: crystal structure of oxyr from porphyromonas gingivalis
30 | c2x7pA_ |
| not modelled | 84.0 | 17 | PDB header:unknown function Chain: A: PDB Molecule:possible thiamine biosynthesis enzyme; PDBTitle: the conserved candida albicans ca3427 gene product defines a new2 family of proteins exhibiting the generic periplasmic binding3 protein structural fold
31 | c2f78A_ |
| not modelled | 82.3 | 34 | PDB header:gene regulation Chain: A: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: benm effector binding domain with its effector benzoate
32 | c3g41A_ |
| not modelled | 77.5 | 14 | PDB header:transport protein Chain: A: PDB Molecule:amino acid abc transporter, periplasmic amino acid-binding PDBTitle: the structure of cpn0482, the arginine binding protein from the2 periplasm of chlamydia pneumoniae
33 | c3delC_ |
| not modelled | 75.1 | 13 | PDB header:protein binding, transport protein Chain: C: PDB Molecule:arginine binding protein; PDBTitle: the structure of ct381, the arginine binding protein from the2 periplasm chlamydia trachomatis
34 | c3n6uA_ |
| not modelled | 74.5 | 15 | PDB header:transcription regulator Chain: A: PDB Molecule:lysr type regulator of tsambcd; PDBTitle: effector binding domain of tsar in complex with its inducer p-2 toluenesulfonate
35 | d2nxoa1 |
| not modelled | 73.9 | 16 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
36 | c3fd3A_ |
| not modelled | 72.6 | 22 | PDB header:transcription regulator Chain: A: PDB Molecule:chromosome replication initiation inhibitor protein; PDBTitle: structure of the c-terminal domains of a lysr family protein from2 agrobacterium tumefaciens str. c58.
37 | d1i6aa_ |
| not modelled | 70.7 | 19 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
38 | c2q2aD_ |
| not modelled | 70.5 | 13 | PDB header:transport protein Chain: D: PDB Molecule:artj; PDBTitle: crystal structures of the arginine-, lysine-, histidine-2 binding protein artj from the thermophilic bacterium3 geobacillus stearothermophilus
39 | c2ylnA_ |
| not modelled | 67.8 | 10 | PDB header:transport protein Chain: A: PDB Molecule:putative abc transporter, periplasmic binding protein, PDBTitle: crystal structure of the l-cystine solute receptor of2 neisseria gonorrhoeae in the closed conformation
40 | d1ixca2 |
| not modelled | 66.9 | 17 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
41 | d1ex2a_ |
| not modelled | 63.8 | 21 | Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:Maf-like
42 | c2p5xB_ |
| not modelled | 60.5 | 21 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:n-acetylserotonin o-methyltransferase-like protein; PDBTitle: crystal structure of maf domain of human n-acetylserotonin o-2 methyltransferase-like protein
43 | c1al3A_ |
| not modelled | 59.4 | 16 | PDB header:transcription regulation Chain: A: PDB Molecule:cys regulon transcriptional activator cysb; PDBTitle: cofactor binding fragment of cysb from klebsiella aerogenes
44 | d1al3a_ |
| not modelled | 59.4 | 16 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
45 | c2o1mB_ |
| not modelled | 56.7 | 15 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:probable amino-acid abc transporter PDBTitle: crystal structure of the probable amino-acid abc2 transporter extracellular-binding protein ytmk from3 bacillus subtilis. northeast structural genomics4 consortium target sr572
46 | c3r39A_ |
| not modelled | 54.0 | 8 | PDB header:transport protein Chain: A: PDB Molecule:putative periplasmic binding protein; PDBTitle: crystal structure of periplasmic d-alanine abc transporter from2 salmonella enterica
47 | d2amha1 |
| not modelled | 52.4 | 30 | Fold:Anticodon-binding domain-like Superfamily:ITPase-like Family:Maf-like
48 | c2pfzA_ |
| not modelled | 49.3 | 18 | PDB header:transport protein Chain: A: PDB Molecule:putative exported protein; PDBTitle: crystal structure of dctp6, a bordetella pertussis2 extracytoplasmic solute receptor binding pyroglutamic acid
49 | c2y7iB_ |
| not modelled | 49.2 | 13 | PDB header:arginine-binding protein Chain: B: PDB Molecule:stm4351; PDBTitle: structural basis for high arginine specificity in salmonella2 typhimurium periplasmic binding protein stm4351.
50 | c2hpgB_ |
| not modelled | 44.4 | 13 | PDB header:ligand binding protein Chain: B: PDB Molecule:abc transporter, periplasmic substrate-binding PDBTitle: the crystal structure of a thermophilic trap periplasmic2 binding protein
51 | d1r9la_ |
| not modelled | 44.0 | 13 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
52 | c2de4B_ |
| not modelled | 41.3 | 13 | PDB header:hydrolase Chain: B: PDB Molecule:dibenzothiophene desulfurization enzyme b; PDBTitle: crystal structure of dszb c27s mutant in complex with biphenyl-2-2 sulfinic acid
53 | c1twyG_ |
| not modelled | 39.7 | 27 | PDB header:structural genomics, unknown function Chain: G: PDB Molecule:abc transporter, periplasmic substrate-binding protein; PDBTitle: crystal structure of an abc-type phosphate transport receptor from2 vibrio cholerae
54 | d1twya_ |
| not modelled | 39.7 | 27 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
55 | c3r6uA_ |
| not modelled | 39.2 | 16 | PDB header:transport protein Chain: A: PDB Molecule:choline-binding protein; PDBTitle: crystal structure of choline binding protein opubc from bacillus2 subtilis
56 | d1tjna_ |
| not modelled | 37.0 | 13 | Fold:Chelatase-like Superfamily:Chelatase Family:CbiX-like
57 | c1tjnA_ |
| not modelled | 37.0 | 13 | PDB header:lyase Chain: A: PDB Molecule:sirohydrochlorin cobaltochelatase; PDBTitle: crystal structure of hypothetical protein af0721 from archaeoglobus2 fulgidus
58 | c2i4cA_ |
| not modelled | 36.8 | 15 | PDB header:transport protein Chain: A: PDB Molecule:bicarbonate transporter; PDBTitle: crystal structure of bicarbonate transport protein cmpa from2 synechocystis sp. pcc 6803 in complex with bicarbonate and calcium
59 | c2rejA_ |
| not modelled | 36.4 | 10 | PDB header:choline-binding protein Chain: A: PDB Molecule:putative glycine betaine abc transporter protein; PDBTitle: abc-transporter choline binding protein in unliganded semi-2 closed conformation
60 | c3hv1A_ |
| not modelled | 35.7 | 12 | PDB header:transport protein Chain: A: PDB Molecule:polar amino acid abc uptake transporter substrate PDBTitle: crystal structure of a polar amino acid abc uptake2 transporter substrate binding protein from streptococcus3 thermophilus
61 | c3n5lA_ |
| not modelled | 33.7 | 18 | PDB header:transport protein Chain: A: PDB Molecule:binding protein component of abc phosphonate transporter; PDBTitle: crystal structure of a binding protein component of abc phosphonate2 transporter (pa3383) from pseudomonas aeruginosa at 1.97 a resolution
62 | c3pppA_ |
| not modelled | 32.4 | 16 | PDB header:transport protein Chain: A: PDB Molecule:glycine betaine/carnitine/choline-binding protein; PDBTitle: structures of the substrate-binding protein provide insights into the2 multiple compatible solutes binding specificities of bacillus3 subtilis abc transporter opuc
63 | c3m1pA_ |
| not modelled | 32.2 | 12 | PDB header:isomerase Chain: A: PDB Molecule:ribose 5-phosphate isomerase; PDBTitle: structure of ribose 5-phosphate isomerase type b from trypanosoma2 cruzi, soaked with allose-6-phosphate
64 | c3k7pA_ |
| not modelled | 32.2 | 12 | PDB header:isomerase Chain: A: PDB Molecule:ribose 5-phosphate isomerase; PDBTitle: structure of mutant of ribose 5-phosphate isomerase type b from2 trypanosoma cruzi.
65 | c2uyeA_ |
| not modelled | 32.1 | 16 | PDB header:transcription Chain: A: PDB Molecule:regulatory protein; PDBTitle: double mutant y110s,f111v dntr from burkholderia sp. strain2 dnt in complex with thiocyanate
66 | c3onmB_ |
| not modelled | 31.2 | 15 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator lrha; PDBTitle: effector binding domain of lysr-type transcription factor rovm from y.2 pseudotuberculosis
67 | d2esna2 |
| not modelled | 30.4 | 23 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
68 | d1hsla_ |
| not modelled | 29.6 | 14 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
69 | c2vd3B_ |
| not modelled | 29.2 | 16 | PDB header:transferase Chain: B: PDB Molecule:atp phosphoribosyltransferase; PDBTitle: the structure of histidine inhibited hisg from2 methanobacterium thermoautotrophicum
70 | c2dlnA_ |
| not modelled | 29.0 | 22 | PDB header:ligase(peptidoglycan synthesis) Chain: A: PDB Molecule:d-alanine--d-alanine ligase; PDBTitle: vancomycin resistance: structure of d-alanine:d-alanine2 ligase at 2.3 angstroms resolution
71 | d1mo0a_ |
| not modelled | 27.3 | 13 | Fold:TIM beta/alpha-barrel Superfamily:Triosephosphate isomerase (TIM) Family:Triosephosphate isomerase (TIM)
72 | c2ieeB_ |
| not modelled | 26.5 | 11 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:probable abc transporter extracellular-binding PDBTitle: crystal structure of yckb_bacsu from bacillus subtilis.2 northeast structural genomics consortium target sr574.
73 | d2a5sa1 |
| not modelled | 24.4 | 18 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
74 | c2h9qC_ |
| not modelled | 22.6 | 13 | PDB header:transcription Chain: C: PDB Molecule:hth-type transcriptional regulator catm; PDBTitle: crystal structure of the effector binding domain of a catm2 variant (r156h)
75 | d1vhca_ |
| not modelled | 22.0 | 15 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase
76 | c2ql3G_ |
| not modelled | 22.0 | 15 | PDB header:transcription Chain: G: PDB Molecule:probable transcriptional regulator, lysr family protein; PDBTitle: crystal structure of the c-terminal domain of a probable lysr family2 transcriptional regulator from rhodococcus sp. rha1
77 | c3i6vA_ |
| not modelled | 21.8 | 16 | PDB header:transport protein Chain: A: PDB Molecule:periplasmic his/glu/gln/arg/opine family-binding protein; PDBTitle: crystal structure of a periplasmic his/glu/gln/arg/opine family-2 binding protein from silicibacter pomeroyi in complex with lysine
78 | c1wloA_ |
| not modelled | 20.7 | 27 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:sufe protein; PDBTitle: solution structure of the hypothetical protein from thermus2 thermophilus hb8
79 | c2jl8S_ |
| not modelled | 20.2 | 22 | PDB header:ribosome Chain: S: PDB Molecule:50s ribosomal protein l18; PDBTitle: insights into translational termination from the structure2 of rf2 bound to the ribosome (part 4 of 4).3 this file contains the 50s subunit.
80 | c2hxrA_ |
| not modelled | 19.9 | 15 | PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional regulator cynr; PDBTitle: structure of the ligand binding domain of e. coli cynr, a2 transcriptional regulator controlling cyanate metabolism
81 | d1sw5a_ |
| not modelled | 19.5 | 15 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
82 | c3k6gA_ |
| not modelled | 19.5 | 15 | PDB header:protein binding Chain: A: PDB Molecule:telomeric repeat-binding factor 2-interacting protein 1; PDBTitle: crystal structure of rap1 and trf2 complex
83 | c3k4uA_ |
| not modelled | 19.2 | 11 | PDB header:transport protein Chain: A: PDB Molecule:binding component of abc transporter; PDBTitle: crystal structure of putative binding component of abc transporter2 from wolinella succinogenes dsm 1740 complexed with lysine
84 | d1t5ba_ |
| not modelled | 19.0 | 8 | Fold:Flavodoxin-like Superfamily:Flavoproteins Family:Quinone reductase
85 | d1us5a_ |
| not modelled | 17.6 | 9 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
86 | c3cz6A_ |
| not modelled | 17.6 | 20 | PDB header:protein binding Chain: A: PDB Molecule:dna-binding protein rap1; PDBTitle: crystal structure of the rap1 c-terminus
87 | d1mzga_ |
| not modelled | 17.5 | 20 | Fold:SufE/NifU Superfamily:SufE/NifU Family:SufE-like
88 | d1lsta_ |
| not modelled | 17.2 | 14 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
89 | d1ni7a_ |
| not modelled | 17.0 | 18 | Fold:SufE/NifU Superfamily:SufE/NifU Family:SufE-like
90 | c3oxnD_ |
| not modelled | 16.8 | 14 | PDB header:transcription regulator Chain: D: PDB Molecule:putative transcriptional regulator, lysr family; PDBTitle: the crystal structure of a putative transcriptional regulator from2 vibrio parahaemolyticus
91 | c3sc6F_ |
| not modelled | 16.7 | 13 | PDB header:oxidoreductase Chain: F: PDB Molecule:dtdp-4-dehydrorhamnose reductase; PDBTitle: 2.65 angstrom resolution crystal structure of dtdp-4-dehydrorhamnose2 reductase (rfbd) from bacillus anthracis str. ames in complex with3 nadp
92 | c2wfoA_ |
| not modelled | 16.1 | 25 | PDB header:viral protein Chain: A: PDB Molecule:glycoprotein 1; PDBTitle: crystal structure of machupo virus envelope glycoprotein2 gp1
93 | c3kosA_ |
| not modelled | 16.0 | 14 | PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional activator ampr; PDBTitle: structure of the ampr effector binding domain from citrobacter2 freundii
94 | d2auna1 |
| not modelled | 15.6 | 22 | Fold:The "swivelling" beta/beta/alpha domain Superfamily:LD-carboxypeptidase A C-terminal domain-like Family:LD-carboxypeptidase A C-terminal domain-like
95 | c3hhfB_ |
| not modelled | 14.9 | 24 | PDB header:transcription regulator Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: structure of crga regulatory domain, a lysr-type transcriptional2 regulator from neisseria meningitidis.
96 | d1khia2 |
| not modelled | 13.9 | 27 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like
97 | c3jv9B_ |
| not modelled | 13.5 | 13 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: the structure of a reduced form of oxyr from n. meningitidis
98 | c2f5zK_ |
| not modelled | 13.4 | 40 | PDB header:oxidoreductase/protein binding Chain: K: PDB Molecule:pyruvate dehydrogenase protein x component; PDBTitle: crystal structure of human dihydrolipoamide dehydrogenase2 (e3) complexed to the e3-binding domain of human e3-3 binding protein
99 | c1zy8M_ |
| not modelled | 13.1 | 40 | PDB header:oxidoreductase Chain: M: PDB Molecule:pyruvate dehydrogenase protein x component, PDBTitle: the crystal structure of dihydrolipoamide dehydrogenase and2 dihydrolipoamide dehydrogenase-binding protein (didomain)3 subcomplex of human pyruvate dehydrogenase complex.

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

Transmembrane helix prediction |

Transmembrane helices have been predicted in your sequence to adopt the topology shown below

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
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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