Phyre 2 Results for P37902

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Email | l.a.kelley@imperial.ac.uk
Description | P37902
Date | Thu Jan 5 11:57:43 GMT 2012
Unique Job ID | b5b984b7bb33ab28

Summary |

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

Model (left) based on template c2vhaB_
Top template information
PDB header:transport protein Chain: B: PDB Molecule:periplasmic binding transport protein; PDBTitle: debp
Confidence and coverage
Confidence: | 100.0% | Coverage: | 91%
276 residues ( 91% 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 | Q | L | R | K | P | A | T | A | I | L | A | L | A | L | S | A | G | L | A | Q | A | D | D | A | A | P | A | A | G | S | T | L | D | K | I | A | K | N | G | V | I | V | V | G | H | R | E | S | S | V | P | F | S | Y | Y | D | N | Q | Q
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | K | V | V | G | Y | S | Q | D | Y | S | N | A | I | V | E | A | V | K | K | K | L | N | K | P | D | L | Q | V | K | L | I | P | I | T | S | Q | N | R | I | P | L | L | Q | N | G | T | F | D | F | E | C | G | S | T | T | N | N | V | E | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | Q | K | Q | A | A | F | S | D | T | I | F | V | V | G | T | R | L | L | T | K | K | G | G | D | I | K | D | F | A | N | L | K | D | K | A | V | V | V | T | S | G | T | T | S | E | V | L | L | N | K | L | N | E | E | Q | K | M | N | M | R
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | I | I | S | A | K | D | H | G | D | S | F | R | T | L | E | S | G | R | A | V | A | F | M | M | D | D | A | L | L | A | G | E | R | A | K | A | K | K | P | D | N | W | E | I | V | G | K | P | Q | S | Q | E | A | Y | G | C | M | L | R | K
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | D | D | P | Q | F | K | K | L | M | D | D | T | I | A | Q | V | Q | T | S | G | E | A | E | K | W | F | D | K | W | F | K | N | P | I | P | P | K | N | L | N | M | N | F | E | L | S | D | E | M | K | A | L | F | K | E | P | N | D | K | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  | ? | ? | ? | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | .
Sequence |  | L | N
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 |
| c2vhaB_ |

### PDB 2vha chain B

Region: 26 - 301
Aligned: 276
Modelled: 276
Confidence: 100.0%
Identity: 99%
PDB header:transport protein
Chain: B: PDB Molecule:periplasmic binding transport protein;
PDBTitle: debp

Phyre2
2 |
| c3hv1A_ |

### PDB 3hv1 chain A

Region: 24 - 281
Aligned: 251
Modelled: 251
Confidence: 100.0%
Identity: 20%
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

Phyre2
3 |
| c2ylnA_ |

### PDB 2yln chain A

Region: 29 - 278
Aligned: 238
Modelled: 244
Confidence: 100.0%
Identity: 16%
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

Phyre2
4 |
| c2ieeB_ |

### PDB 2iee chain B

Region: 33 - 287
Aligned: 244
Modelled: 248
Confidence: 100.0%
Identity: 15%
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.

Phyre2
5 |
| c3k4uA_ |

### PDB 3k4u chain A

Region: 39 - 273
Aligned: 227
Modelled: 235
Confidence: 100.0%
Identity: 22%
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

Phyre2
6 |
| c3g41A_ |

### PDB 3g41 chain A

Region: 38 - 277
Aligned: 230
Modelled: 239
Confidence: 100.0%
Identity: 16%
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

Phyre2
7 |
| c1xt8B_ |

### PDB 1xt8 chain B

Region: 27 - 282
Aligned: 246
Modelled: 252
Confidence: 100.0%
Identity: 21%
PDB header:transport protein
Chain: B: PDB Molecule:putative amino-acid transporter periplasmic solute-binding
PDBTitle: crystal structure of cysteine-binding protein from campylobacter2 jejuni at 2.0 a resolution

Phyre2
8 |
| c2v25B_ |

### PDB 2v25 chain B

Region: 32 - 272
Aligned: 230
Modelled: 236
Confidence: 100.0%
Identity: 24%
PDB header:receptor
Chain: B: PDB Molecule:major cell-binding factor;
PDBTitle: structure of the campylobacter jejuni antigen peb1a, an2 aspartate and glutamate receptor with bound aspartate

Phyre2
9 |
| c2yjpB_ |

### PDB 2yjp chain B

Region: 31 - 282
Aligned: 242
Modelled: 248
Confidence: 100.0%
Identity: 24%
PDB header:transport protein
Chain: B: PDB Molecule:putative abc transporter, periplasmic binding protein,
PDBTitle: crystal structure of the solute receptors for l-cysteine of2 neisseria gonorrhoeae

Phyre2
10 |
| d1hsla_ |

### PDB 1hsl chain A

Region: 39 - 274
Aligned: 228
Modelled: 236
Confidence: 100.0%
Identity: 21%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2
11 |
| c3kbrA_ |

### PDB 3kbr chain A

Region: 30 - 270
Aligned: 231
Modelled: 234
Confidence: 100.0%
Identity: 21%
PDB header:lyase
Chain: A: PDB Molecule:cyclohexadienyl dehydratase;
PDBTitle: the crystal structure of cyclohexadienyl dehydratase precursor from2 pseudomonas aeruginosa pa01

Phyre2
12 |
| d1xt8a1 |

### PDB 1xt8 chain A domain 1

Region: 31 - 282
Aligned: 242
Modelled: 248
Confidence: 100.0%
Identity: 21%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2
13 |
| c2q89A_ |

### PDB 2q89 chain A

Region: 29 - 282
Aligned: 246
Modelled: 247
Confidence: 100.0%
Identity: 18%
PDB header:transport protein
Chain: A: PDB Molecule:putative abc transporter amino acid-binding protein;
PDBTitle: crystal structure of ehub in complex with hydroxyectoine

Phyre2
14 |
| d1lsta_ |

### PDB 1lst chain A

Region: 39 - 275
Aligned: 229
Modelled: 237
Confidence: 100.0%
Identity: 20%
Fold: Periplasmic binding protein-like II
Superfamily: Periplasmic binding protein-like II
Family: Phosphate binding protein-like

Phyre2
15 |
| c3delC_ |

### PDB 3del chain C

Region: 40 - 278
Aligned: 228
Modelled: 239
Confidence: 100.0%
Identity: 15%
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

Phyre2
16 |
| c2q2aD_ |

### PDB 2q2a chain D

Region: 37 - 275
Aligned: 228
Modelled: 239
Confidence: 100.0%
Identity: 23%
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

Phyre2
17 |
| c3h7mA_ |

### PDB 3h7m chain A

Region: 38 - 275
Aligned: 226
Modelled: 238
Confidence: 100.0%
Identity: 16%
PDB header:transferase
Chain: A: PDB Molecule:sensor protein;
PDBTitle: crystal structure of a histidine kinase sensor domain with2 similarity to periplasmic binding proteins

Phyre2
18 |
| c2o1mB_ |

### PDB 2o1m chain B

Region: 38 - 272
Aligned: 224
Modelled: 235
Confidence: 100.0%
Identity: 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

Phyre2
19 |
| c3i6vA_ |

### PDB 3i6v chain A

Region: 41 - 277
Aligned: 218
Modelled: 237
Confidence: 100.0%
Identity: 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

Phyre2
20 |
| c3r39A_ |

### PDB 3r39 chain A

Region: 36 - 272
Aligned: 226
Modelled: 237
Confidence: 100.0%
Identity: 12%
PDB header:transport protein
Chain: A: PDB Molecule:putative periplasmic binding protein;
PDBTitle: crystal structure of periplasmic d-alanine abc transporter from2 salmonella enterica

Phyre2
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98 |
99 |

Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c2vhaB_ |
|  | 100.0 | 99 | PDB header:transport protein Chain: B: PDB Molecule:periplasmic binding transport protein; PDBTitle: debp
2 | c3hv1A_ |
|  | 100.0 | 20 | 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
3 | c2ylnA_ |
|  | 100.0 | 16 | 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
4 | c2ieeB_ |
|  | 100.0 | 15 | 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.
5 | c3k4uA_ |
|  | 100.0 | 22 | 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
6 | c3g41A_ |
|  | 100.0 | 16 | 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
7 | c1xt8B_ |
|  | 100.0 | 21 | PDB header:transport protein Chain: B: PDB Molecule:putative amino-acid transporter periplasmic solute-binding PDBTitle: crystal structure of cysteine-binding protein from campylobacter2 jejuni at 2.0 a resolution
8 | c2v25B_ |
|  | 100.0 | 24 | PDB header:receptor Chain: B: PDB Molecule:major cell-binding factor; PDBTitle: structure of the campylobacter jejuni antigen peb1a, an2 aspartate and glutamate receptor with bound aspartate
9 | c2yjpB_ |
|  | 100.0 | 24 | PDB header:transport protein Chain: B: PDB Molecule:putative abc transporter, periplasmic binding protein, PDBTitle: crystal structure of the solute receptors for l-cysteine of2 neisseria gonorrhoeae
10 | d1hsla_ |
|  | 100.0 | 21 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
11 | c3kbrA_ |
|  | 100.0 | 21 | PDB header:lyase Chain: A: PDB Molecule:cyclohexadienyl dehydratase; PDBTitle: the crystal structure of cyclohexadienyl dehydratase precursor from2 pseudomonas aeruginosa pa01
12 | d1xt8a1 |
|  | 100.0 | 21 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
13 | c2q89A_ |
|  | 100.0 | 18 | PDB header:transport protein Chain: A: PDB Molecule:putative abc transporter amino acid-binding protein; PDBTitle: crystal structure of ehub in complex with hydroxyectoine
14 | d1lsta_ |
|  | 100.0 | 20 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
15 | c3delC_ |
|  | 100.0 | 15 | 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
16 | c2q2aD_ |
|  | 100.0 | 23 | 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
17 | c3h7mA_ |
|  | 100.0 | 16 | PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of a histidine kinase sensor domain with2 similarity to periplasmic binding proteins
18 | c2o1mB_ |
|  | 100.0 | 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
19 | c3i6vA_ |
|  | 100.0 | 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
20 | c3r39A_ |
|  | 100.0 | 12 | PDB header:transport protein Chain: A: PDB Molecule:putative periplasmic binding protein; PDBTitle: crystal structure of periplasmic d-alanine abc transporter from2 salmonella enterica
21 | c2y7iB_ |
| not modelled | 100.0 | 20 | PDB header:arginine-binding protein Chain: B: PDB Molecule:stm4351; PDBTitle: structural basis for high arginine specificity in salmonella2 typhimurium periplasmic binding protein stm4351.
22 | c3kzgB_ |
| not modelled | 100.0 | 19 | 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
23 | d1wdna_ |
| not modelled | 100.0 | 23 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
24 | d2a5sa1 |
| not modelled | 100.0 | 19 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
25 | c3mplA_ |
| not modelled | 100.0 | 12 | PDB header:signaling protein Chain: A: PDB Molecule:virulence sensor protein bvgs; PDBTitle: crystal structure of bordetella pertussis bvgs vft2 domain (double2 mutant f375e/q461e)
26 | d1mqia_ |
| not modelled | 100.0 | 17 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
27 | c2xx7B_ |
| not modelled | 100.0 | 16 | PDB header:transport protein Chain: B: PDB Molecule:glutamate receptor 2; PDBTitle: crystal structure of 1-(4-(1-pyrrolidinylcarbonyl)phenyl)-3-2 (trifluoromethyl)-4,5,6,7-tetrahydro-1h-indazole in complex with3 the ligand binding domain of the rat glua2 receptor and glutamate4 at 2.2a resolution.
28 | d1pb7a_ |
| not modelled | 100.0 | 19 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
29 | c2rc9A_ |
| not modelled | 100.0 | 23 | PDB header:membrane protein Chain: A: PDB Molecule:glutamate [nmda] receptor subunit 3a; PDBTitle: crystal structure of the nr3a ligand binding core complex with acpc at2 1.96 angstrom resolution
30 | d1ii5a_ |
| not modelled | 100.0 | 17 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
31 | d1s50a1 |
| not modelled | 100.0 | 15 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
32 | c2pyyB_ |
| not modelled | 100.0 | 21 | PDB header:transport protein Chain: B: PDB Molecule:ionotropic glutamate receptor bacterial homologue; PDBTitle: crystal structure of the glur0 ligand-binding core from nostoc2 punctiforme in complex with (l)-glutamate
33 | c2v3tA_ |
| not modelled | 100.0 | 15 | PDB header:receptor Chain: A: PDB Molecule:glutamate receptor delta-2 subunit synonym PDBTitle: structure of the ligand-binding core of the ionotropic2 glutamate receptor-like glurdelta2 in the apo form
34 | d2f34a1 |
| not modelled | 100.0 | 17 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
35 | c1yaeB_ |
| not modelled | 99.9 | 13 | PDB header:membrane protein Chain: B: PDB Molecule:glutamate receptor, ionotropic kainate 2; PDBTitle: structure of the kainate receptor subunit glur6 agonist binding domain2 complexed with domoic acid
36 | c3kg2A_ |
| not modelled | 99.8 | 19 | PDB header:membrane protein, transport protein Chain: A: PDB Molecule:glutamate receptor 2; PDBTitle: ampa subtype ionotropic glutamate receptor in complex with competitive2 antagonist zk 200775
37 | c3n5lA_ |
| not modelled | 98.5 | 15 | 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
38 | c3e4rA_ |
| not modelled | 98.1 | 14 | 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
39 | c2x26A_ |
| not modelled | 98.1 | 15 | 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
40 | c3uifA_ |
| not modelled | 97.9 | 14 | 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
41 | c3un6A_ |
| not modelled | 97.7 | 11 | 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
42 | c3l6gA_ |
| not modelled | 97.6 | 11 | 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
43 | c3ix1A_ |
| not modelled | 97.6 | 13 | 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
44 | c3ix1B_ |
| not modelled | 97.6 | 13 | 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
45 | c3tqwA_ |
| not modelled | 97.6 | 14 | PDB header:transport protein Chain: A: PDB Molecule:methionine-binding protein; PDBTitle: structure of a abc transporter, periplasmic substrate-binding protein2 from coxiella burnetii
46 | d1xs5a_ |
| not modelled | 97.5 | 10 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
47 | c3k2dA_ |
| not modelled | 97.1 | 11 | 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
48 | d1p99a_ |
| not modelled | 97.1 | 15 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
49 | c1p99A_ |
| not modelled | 97.1 | 15 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pg110; PDBTitle: 1.7a crystal structure of protein pg110 from staphylococcus2 aureus
50 | c3hn0A_ |
| not modelled | 97.1 | 9 | 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
51 | c3tmgA_ |
| not modelled | 96.9 | 13 | 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
52 | c2x7pA_ |
| not modelled | 96.8 | 10 | 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
53 | c3gxaA_ |
| not modelled | 95.9 | 16 | PDB header:protein binding Chain: A: PDB Molecule:outer membrane lipoprotein gna1946; PDBTitle: crystal structure of gna1946
54 | c2dvzA_ |
| not modelled | 95.6 | 13 | PDB header:transport protein Chain: A: PDB Molecule:putative exported protein; PDBTitle: structure of a periplasmic transporter
55 | c3ir1F_ |
| not modelled | 95.5 | 12 | PDB header:protein binding Chain: F: PDB Molecule:outer membrane lipoprotein gna1946; PDBTitle: crystal structure of lipoprotein gna1946 from neisseria2 meningitidis
56 | c2de4B_ |
| not modelled | 95.3 | 12 | 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
57 | c3qslA_ |
| not modelled | 95.2 | 16 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative exported protein; PDBTitle: structure of cae31940 from bordetella bronchiseptica rb50
58 | c2f5xC_ |
| not modelled | 94.5 | 11 | PDB header:transport protein Chain: C: PDB Molecule:bugd; PDBTitle: structure of periplasmic binding protein bugd
59 | d1us5a_ |
| not modelled | 94.0 | 13 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
60 | c2ql3G_ |
| not modelled | 92.8 | 12 | 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
61 | c2g29A_ |
| not modelled | 92.3 | 12 | PDB header:transport protein Chain: A: PDB Molecule:nitrate transport protein nrta; PDBTitle: crystal structure of the periplasmic nitrate-binding2 protein nrta from synechocystis pcc 6803
62 | c2qpqC_ |
| not modelled | 92.3 | 15 | PDB header:transport protein Chain: C: PDB Molecule:protein bug27; PDBTitle: structure of bug27 from bordetella pertussis
63 | c2i4cA_ |
| not modelled | 91.3 | 12 | 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
64 | c3ho7A_ |
| not modelled | 90.8 | 13 | PDB header:transcription Chain: A: PDB Molecule:oxyr; PDBTitle: crystal structure of oxyr from porphyromonas gingivalis
65 | d2nxoa1 |
| not modelled | 85.9 | 11 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
66 | c3oxnD_ |
| not modelled | 85.3 | 7 | 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
67 | d1al3a_ |
| not modelled | 84.0 | 12 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
68 | c1al3A_ |
| not modelled | 84.0 | 12 | PDB header:transcription regulation Chain: A: PDB Molecule:cys regulon transcriptional activator cysb; PDBTitle: cofactor binding fragment of cysb from klebsiella aerogenes
69 | c3n6uA_ |
| not modelled | 81.9 | 12 | 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
70 | d2czla1 |
| not modelled | 81.3 | 10 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
71 | d2fyia1 |
| not modelled | 80.1 | 14 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
72 | d1zbma1 |
| not modelled | 79.6 | 10 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
73 | c2rejA_ |
| not modelled | 79.0 | 15 | 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
74 | c3jv9B_ |
| not modelled | 75.5 | 11 | PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: the structure of a reduced form of oxyr from n. meningitidis
75 | d1i6aa_ |
| not modelled | 74.3 | 12 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
76 | c3lr1A_ |
| not modelled | 65.6 | 10 | PDB header:transport protein Chain: A: PDB Molecule:tungstate abc transporter, periplasmic tungstate- PDBTitle: the crystal structure of the tungstate abc transporter from2 geobacter sulfurreducens
77 | c2h9qC_ |
| not modelled | 61.3 | 11 | 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)
78 | c2f7cA_ |
| not modelled | 61.1 | 11 | PDB header:gene regulation Chain: A: PDB Molecule:hth-type transcriptional regulator catm; PDBTitle: catm effector binding domain with its effector cis,cis-muconate
79 | c2f78A_ |
| not modelled | 59.7 | 12 | PDB header:gene regulation Chain: A: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: benm effector binding domain with its effector benzoate
80 | d1utha_ |
| not modelled | 49.5 | 10 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
81 | c2uyeA_ |
| not modelled | 46.4 | 9 | PDB header:transcription Chain: A: PDB Molecule:regulatory protein; PDBTitle: double mutant y110s,f111v dntr from burkholderia sp. strain2 dnt in complex with thiocyanate
82 | c3r6uA_ |
| not modelled | 35.3 | 13 | PDB header:transport protein Chain: A: PDB Molecule:choline-binding protein; PDBTitle: crystal structure of choline binding protein opubc from bacillus2 subtilis
83 | d1ixca2 |
| not modelled | 32.8 | 11 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
84 | c1hfeT_ |
| not modelled | 30.5 | 10 | PDB header:hydrogenase Chain: T: PDB Molecule:protein (fe-only hydrogenase (e.c.1.18.99.1) PDBTitle: 1.6 a resolution structure of the fe-only hydrogenase from2 desulfovibrio desulfuricans
85 | d1hfes_ |
| not modelled | 30.5 | 10 | Fold:Non-globular all-alpha subunits of globular proteins Superfamily:Fe-only hydrogenase smaller subunit Family:Fe-only hydrogenase smaller subunit
86 | c2h9bB_ |
| not modelled | 28.8 | 13 | 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)
87 | d1atga_ |
| not modelled | 25.7 | 13 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
88 | d2ozza1 |
| not modelled | 24.2 | 13 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
89 | c3fd3A_ |
| not modelled | 21.9 | 9 | 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.
90 | c3eplA_ |
| not modelled | 20.6 | 12 | PDB header:transferase/rna Chain: A: PDB Molecule:trna isopentenyltransferase; PDBTitle: crystallographic snapshots of eukaryotic2 dimethylallyltransferase acting on trna: insight into trna3 recognition and reaction mechanism
91 | d2esna2 |
| not modelled | 16.7 | 9 | Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like
92 | c2vd3B_ |
| not modelled | 16.3 | 9 | PDB header:transferase Chain: B: PDB Molecule:atp phosphoribosyltransferase; PDBTitle: the structure of histidine inhibited hisg from2 methanobacterium thermoautotrophicum
93 | c2esnC_ |
| not modelled | 15.9 | 12 | PDB header:structural genomics, unknown function Chain: C: PDB Molecule:probable transcriptional regulator; PDBTitle: the crystal structure of probable transcriptional regulator pa04772 from pseudomonas aeruginosa
94 | c3muqB_ |
| not modelled | 12.9 | 10 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized conserved protein; PDBTitle: the crystal structure of a conserved functionally unknown protein from2 vibrio parahaemolyticus rimd 2210633
95 | d1g12a_ |
| not modelled | 12.7 | 17 | Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Fungal zinc peptidase
96 | c3chgB_ |
| not modelled | 12.2 | 16 | PDB header:ligand binding protein Chain: B: PDB Molecule:glycine betaine-binding protein; PDBTitle: the compatible solute-binding protein opuac from bacillus2 subtilis in complex with dmsa
97 | c3fj7A_ |
| not modelled | 12.0 | 11 | PDB header:protein binding Chain: A: PDB Molecule:major antigenic peptide peb3; PDBTitle: crystal structure of l-phospholactate bound peb3
98 | c3hhfB_ |
| not modelled | 11.9 | 11 | 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.
99 | c1jvnB_ |
| not modelled | 10.7 | 22 | PDB header:transferase Chain: B: PDB Molecule:bifunctional histidine biosynthesis protein hishf; PDBTitle: crystal structure of imidazole glycerol phosphate synthase: a tunnel2 through a (beta/alpha)8 barrel joins two active sites

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
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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