Phyre 2 Results for P39220

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Email | l.a.kelley@imperial.ac.uk
Description | P39220
Date | Thu Jan 5 11:58:32 GMT 2012
Unique Job ID | 5b6999045ef68bf5

Summary |

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

Model (left) based on template c3cxbA_
Top template information
PDB header:signaling protein Chain: A: PDB Molecule:protein sifa; PDBTitle: crystal structure of sifa and skip
Confidence and coverage
Confidence: | 96.6% | Coverage: | 24%
52 residues ( 24% of your sequence) have been modelled with 96.6% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
3D viewing
Interactive 3D view in Jmol

Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | K | V | S | V | P | G | M | P | V | T | L | L | N | M | S | K | N | D | I | Y | K | M | V | S | G | D | K | M | D | V | K | M | N | I | F | Q | R | L | W | E | T | L | R | H | L | F | W | S | D | K | Q | T | E | A | Y | K | L | L | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  | ? | ? | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | N | F | V | N | N | Q | T | G | N | I | N | A | S | E | Y | F | T | G | A | I | N | E | N | E | R | E | K | F | I | N | S | L | E | L | F | N | K | L | K | T | C | A | K | N | P | D | E | L | V | A | K | G | N | M | R | W | V | A | Q | T
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  | ? | ? |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |  |  |  |  | ?
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | F | G | D | I | E | L | S | V | T | F | F | I | E | K | N | K | I | C | T | Q | T | L | Q | L | H | K | G | Q | G | N | L | G | V | D | L | R | K | A | Y | L | P | G | V | D | M | R | D | C | Y | L | G | K | K | T | M | K | G | S | N | D
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  | ? | ? |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | .
Sequence |  | I | L | Y | E | R | P | G | W | N | A | N | L | G | V | L | P | R | T | V | L | P | R | T | V | L | T | R | T | V | L | T | W | T | V | L | P
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 |
| c3cxbA_ |

### PDB 3cxb chain A

Region: 34 - 102
Aligned: 52
Modelled: 52
Confidence: 96.6%
Identity: 23%
PDB header:signaling protein
Chain: A: PDB Molecule:protein sifa;
PDBTitle: crystal structure of sifa and skip

Phyre2
2 |
| c3n90A_ |

### PDB 3n90 chain A

Region: 152 - 179
Aligned: 28
Modelled: 28
Confidence: 47.0%
Identity: 18%
PDB header:unknown function
Chain: A: PDB Molecule:thylakoid lumenal 15 kda protein 1, chloroplastic;
PDBTitle: the 1.7 angstrom resolution crystal structure of at2g44920, a2 pentapeptide repeat protein from arabidopsis thaliana thylakoid3 lumen.

Phyre2
3 |
| d2j8ia1 |

### PDB 2j8i chain A domain 1

Region: 152 - 215
Aligned: 64
Modelled: 64
Confidence: 43.0%
Identity: 20%
Fold: Single-stranded right-handed beta-helix
Superfamily: Pentapeptide repeat-like
Family: Pentapeptide repeats

Phyre2
4 |
| c1v0dA_ |

### PDB 1v0d chain A

Region: 18 - 98
Aligned: 76
Modelled: 81
Confidence: 32.0%
Identity: 22%
PDB header:hydrolase
Chain: A: PDB Molecule:dna fragmentation factor 40 kda subunit;
PDBTitle: crystal structure of caspase-activated dnase (cad)

Phyre2
5 |
| d1v0da_ |

### PDB 1v0d chain A

Region: 18 - 98
Aligned: 76
Modelled: 81
Confidence: 32.0%
Identity: 22%
Fold: His-Me finger endonucleases
Superfamily: His-Me finger endonucleases
Family: Caspase-activated DNase, CAD (DffB, DFF40)

Phyre2
6 |
| d2fvka1 |

### PDB 2fvk chain A domain 1

Region: 122 - 213
Aligned: 91
Modelled: 92
Confidence: 27.0%
Identity: 14%
Fold: Composite domain of metallo-dependent hydrolases
Superfamily: Composite domain of metallo-dependent hydrolases
Family: Hydantoinase (dihydropyrimidinase)

Phyre2
7 |
| d2j8ka1 |

### PDB 2j8k chain A domain 1

Region: 152 - 179
Aligned: 28
Modelled: 28
Confidence: 25.0%
Identity: 29%
Fold: Single-stranded right-handed beta-helix
Superfamily: Pentapeptide repeat-like
Family: Pentapeptide repeats

Phyre2
8 |
| c2j8iB_ |

### PDB 2j8i chain B

Region: 152 - 215
Aligned: 64
Modelled: 64
Confidence: 18.1%
Identity: 20%
PDB header:toxin
Chain: B: PDB Molecule:np275;
PDBTitle: structure of np275, a pentapeptide repeat protein from2 nostoc punctiforme

Phyre2
9 |
| c2xtwB_ |

### PDB 2xtw chain B

Region: 152 - 194
Aligned: 43
Modelled: 43
Confidence: 15.9%
Identity: 14%
PDB header:cell cycle
Chain: B: PDB Molecule:qnrb1;
PDBTitle: structure of qnrb1 (full length), a plasmid-mediated2 fluoroquinolone resistance protein

Phyre2
10 |
| c2j8kA_ |

### PDB 2j8k chain A

Region: 152 - 179
Aligned: 28
Modelled: 28
Confidence: 15.0%
Identity: 29%
PDB header:toxin
Chain: A: PDB Molecule:np275-np276;
PDBTitle: structure of the fusion of np275 and np276, pentapeptide2 repeat proteins from nostoc punctiforme

Phyre2
11 |
| c3du1X_ |

### PDB 3du1 chain X

Region: 152 - 179
Aligned: 28
Modelled: 28
Confidence: 14.1%
Identity: 29%
PDB header:structural protein
Chain: X: PDB Molecule:all3740 protein;
PDBTitle: the 2.0 angstrom resolution crystal structure of hetl, a pentapeptide2 repeat protein involved in heterocyst differentiation regulation from3 the cyanobacterium nostoc sp. strain pcc 7120

Phyre2
12 |
| c2jx3A_ |

### PDB 2jx3 chain A

Region: 47 - 97
Aligned: 50
Modelled: 51
Confidence: 14.1%
Identity: 24%
PDB header:dna binding protein
Chain: A: PDB Molecule:protein dek;
PDBTitle: nmr solution structure of the n-terminal domain of dek

Phyre2
13 |
| c1soxB_ |

### PDB 1sox chain B

Region: 41 - 71
Aligned: 31
Modelled: 31
Confidence: 13.8%
Identity: 13%
PDB header:oxidoreductase
Chain: B: PDB Molecule:sulfite oxidase;
PDBTitle: sulfite oxidase from chicken liver

Phyre2
14 |
| d1zh5a1 |

### PDB 1zh5 chain A domain 1

Region: 51 - 110
Aligned: 57
Modelled: 60
Confidence: 13.2%
Identity: 14%
Fold: DNA/RNA-binding 3-helical bundle
Superfamily: "Winged helix" DNA-binding domain
Family: La domain

Phyre2
15 |
| c1i8nA_ |

### PDB 1i8n chain A

Region: 177 - 211
Aligned: 25
Modelled: 35
Confidence: 13.1%
Identity: 48%
PDB header:toxin
Chain: A: PDB Molecule:anti-platelet protein;
PDBTitle: crystal structure of leech anti-platelet protein

Phyre2
16 |
| d1i8na_ |

### PDB 1i8n chain A

Region: 177 - 211
Aligned: 25
Modelled: 35
Confidence: 13.1%
Identity: 48%
Fold: Hairpin loop containing domain-like
Superfamily: Hairpin loop containing domain-like
Family: Anti-platelet protein

Phyre2
17 |
| c2o6wA_ |

### PDB 2o6w chain A

Region: 152 - 179
Aligned: 28
Modelled: 28
Confidence: 12.9%
Identity: 18%
PDB header:unknown function
Chain: A: PDB Molecule:repeat five residue (rfr) protein or
PDBTitle: crystal structure of a pentapeptide repeat protein (rfr23)2 from the cyanobacterium cyanothece 51142

Phyre2
18 |
| d2f3la1 |

### PDB 2f3l chain A domain 1

Region: 152 - 200
Aligned: 46
Modelled: 49
Confidence: 11.8%
Identity: 24%
Fold: Single-stranded right-handed beta-helix
Superfamily: Pentapeptide repeat-like
Family: Pentapeptide repeats

Phyre2
19 |
| d1tuaa2 |

### PDB 1tua chain A domain 2

Region: 14 - 42
Aligned: 29
Modelled: 29
Confidence: 11.6%
Identity: 10%
Fold: Eukaryotic type KH-domain (KH-domain type I)
Superfamily: Eukaryotic type KH-domain (KH-domain type I)
Family: Eukaryotic type KH-domain (KH-domain type I)

Phyre2
20 |
| c1nh1A_ |

### PDB 1nh1 chain A

Region: 36 - 46
Aligned: 11
Modelled: 11
Confidence: 11.4%
Identity: 27%
PDB header:avirulence protein
Chain: A: PDB Molecule:avirulence b protein;
PDBTitle: crystal structure of the type iii effector avrb from2 pseudomonas syringae.

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c3cxbA_ |
|  | 96.6 | 23 | PDB header:signaling protein Chain: A: PDB Molecule:protein sifa; PDBTitle: crystal structure of sifa and skip
2 | c3n90A_ |
|  | 47.0 | 18 | PDB header:unknown function Chain: A: PDB Molecule:thylakoid lumenal 15 kda protein 1, chloroplastic; PDBTitle: the 1.7 angstrom resolution crystal structure of at2g44920, a2 pentapeptide repeat protein from arabidopsis thaliana thylakoid3 lumen.
3 | d2j8ia1 |
|  | 43.0 | 20 | Fold:Single-stranded right-handed beta-helix Superfamily:Pentapeptide repeat-like Family:Pentapeptide repeats
4 | c1v0dA_ |
|  | 32.0 | 22 | PDB header:hydrolase Chain: A: PDB Molecule:dna fragmentation factor 40 kda subunit; PDBTitle: crystal structure of caspase-activated dnase (cad)
5 | d1v0da_ |
|  | 32.0 | 22 | Fold:His-Me finger endonucleases Superfamily:His-Me finger endonucleases Family:Caspase-activated DNase, CAD (DffB, DFF40)
6 | d2fvka1 |
|  | 27.0 | 14 | Fold:Composite domain of metallo-dependent hydrolases Superfamily:Composite domain of metallo-dependent hydrolases Family:Hydantoinase (dihydropyrimidinase)
7 | d2j8ka1 |
|  | 25.0 | 29 | Fold:Single-stranded right-handed beta-helix Superfamily:Pentapeptide repeat-like Family:Pentapeptide repeats
8 | c2j8iB_ |
|  | 18.1 | 20 | PDB header:toxin Chain: B: PDB Molecule:np275; PDBTitle: structure of np275, a pentapeptide repeat protein from2 nostoc punctiforme
9 | c2xtwB_ |
|  | 15.9 | 14 | PDB header:cell cycle Chain: B: PDB Molecule:qnrb1; PDBTitle: structure of qnrb1 (full length), a plasmid-mediated2 fluoroquinolone resistance protein
10 | c2j8kA_ |
|  | 15.0 | 29 | PDB header:toxin Chain: A: PDB Molecule:np275-np276; PDBTitle: structure of the fusion of np275 and np276, pentapeptide2 repeat proteins from nostoc punctiforme
11 | c3du1X_ |
|  | 14.1 | 29 | PDB header:structural protein Chain: X: PDB Molecule:all3740 protein; PDBTitle: the 2.0 angstrom resolution crystal structure of hetl, a pentapeptide2 repeat protein involved in heterocyst differentiation regulation from3 the cyanobacterium nostoc sp. strain pcc 7120
12 | c2jx3A_ |
|  | 14.1 | 24 | PDB header:dna binding protein Chain: A: PDB Molecule:protein dek; PDBTitle: nmr solution structure of the n-terminal domain of dek
13 | c1soxB_ |
|  | 13.8 | 13 | PDB header:oxidoreductase Chain: B: PDB Molecule:sulfite oxidase; PDBTitle: sulfite oxidase from chicken liver
14 | d1zh5a1 |
|  | 13.2 | 14 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:La domain
15 | c1i8nA_ |
|  | 13.1 | 48 | PDB header:toxin Chain: A: PDB Molecule:anti-platelet protein; PDBTitle: crystal structure of leech anti-platelet protein
16 | d1i8na_ |
|  | 13.1 | 48 | Fold:Hairpin loop containing domain-like Superfamily:Hairpin loop containing domain-like Family:Anti-platelet protein
17 | c2o6wA_ |
|  | 12.9 | 18 | PDB header:unknown function Chain: A: PDB Molecule:repeat five residue (rfr) protein or PDBTitle: crystal structure of a pentapeptide repeat protein (rfr23)2 from the cyanobacterium cyanothece 51142
18 | d2f3la1 |
|  | 11.8 | 24 | Fold:Single-stranded right-handed beta-helix Superfamily:Pentapeptide repeat-like Family:Pentapeptide repeats
19 | d1tuaa2 |
|  | 11.6 | 10 | Fold:Eukaryotic type KH-domain (KH-domain type I) Superfamily:Eukaryotic type KH-domain (KH-domain type I) Family:Eukaryotic type KH-domain (KH-domain type I)
20 | c1nh1A_ |
|  | 11.4 | 27 | PDB header:avirulence protein Chain: A: PDB Molecule:avirulence b protein; PDBTitle: crystal structure of the type iii effector avrb from2 pseudomonas syringae.
21 | d1nh1a_ |
| not modelled | 11.4 | 27 | Fold:Antivirulence factor Superfamily:Antivirulence factor Family:Antivirulence factor
22 | c3ia0c_ |
| not modelled | 11.3 | 26 | PDB header:structural protein Chain: C: PDB Molecule:ethanolamine utilization protein euts; PDBTitle: ethanolamine utilization microcompartment shell subunit,2 euts-g39v mutant
23 | c2g0yA_ |
| not modelled | 11.1 | 18 | PDB header:unknown function Chain: A: PDB Molecule:pentapeptide repeat protein; PDBTitle: crystal structure of a lumenal pentapeptide repeat protein from2 cyanothece sp 51142 at 2.3 angstrom resolution. tetragonal crystal3 form
24 | c3lo0A_ |
| not modelled | 10.9 | 28 | PDB header:hydrolase Chain: A: PDB Molecule:inorganic pyrophosphatase; PDBTitle: crystal structure of inorganic pyrophosphatase from2 ehrlichia chaffeensis
25 | c2wknE_ |
| not modelled | 10.7 | 31 | PDB header:hydrolase Chain: E: PDB Molecule:formamidase; PDBTitle: gamma lactamase from delftia acidovorans
26 | c2wvmA_ |
| not modelled | 9.6 | 53 | PDB header:transferase Chain: A: PDB Molecule:mannosyl-3-phosphoglycerate synthase; PDBTitle: h309a mutant of mannosyl-3-phosphoglycerate synthase from2 thermus thermophilus hb27 in complex with3 gdp-alpha-d-mannose and mg(ii)
27 | c2xt4B_ |
| not modelled | 9.4 | 14 | PDB header:cell cycle Chain: B: PDB Molecule:mcbg-like protein; PDBTitle: structure of the pentapeptide repeat protein albg, a2 resistance factor for the topoisomerase poison albicidin.
28 | c3ifuA_ |
| not modelled | 9.1 | 26 | PDB header:transcription Chain: A: PDB Molecule:non-structural protein; PDBTitle: the crystal structure of porcine reproductive and2 respiratory syndrome virus (prrsv) leader protease nsp1
29 | d1yj5a1 |
| not modelled | 9.0 | 20 | Fold:HAD-like Superfamily:HAD-like Family:phosphatase domain of polynucleotide kinase
30 | c2xt4A_ |
| not modelled | 8.7 | 11 | PDB header:cell cycle Chain: A: PDB Molecule:mcbg-like protein; PDBTitle: structure of the pentapeptide repeat protein albg, a2 resistance factor for the topoisomerase poison albicidin.
31 | c3mjjD_ |
| not modelled | 8.5 | 26 | PDB header:hydrolase Chain: D: PDB Molecule:predicted acetamidase/formamidase; PDBTitle: crystal structure analysis of a recombinant predicted2 acetamidase/formamidase from the thermophile thermoanaerobacter3 tengcongensis
32 | d1isia_ |
| not modelled | 8.4 | 21 | Fold:Flavodoxin-like Superfamily:N-(deoxy)ribosyltransferase-like Family:ADP ribosyl cyclase-like
33 | d1j2za_ |
| not modelled | 8.4 | 15 | Fold:Single-stranded left-handed beta-helix Superfamily:Trimeric LpxA-like enzymes Family:UDP N-acetylglucosamine acyltransferase
34 | c2w7zB_ |
| not modelled | 8.3 | 21 | PDB header:inhibitor Chain: B: PDB Molecule:pentapeptide repeat family protein; PDBTitle: structure of the pentapeptide repeat protein efsqnr, a dna2 gyrase inhibitor. free amines modified by cyclic3 pentylation with glutaraldehyde.
35 | c3t2dA_ |
| not modelled | 8.0 | 41 | PDB header:lyase, hydrolase Chain: A: PDB Molecule:fructose-1,6-bisphosphate aldolase/phosphatase; PDBTitle: fructose-1,6-bisphosphate aldolase/phosphatase from thermoproteus2 neutrophilus, fbp-bound form
36 | c1jrjA_ |
| not modelled | 8.0 | 26 | PDB header:hormone/growth factor Chain: A: PDB Molecule:exendin-4; PDBTitle: solution structure of exendin-4 in 30-vol% trifluoroethanol
37 | c3b9eA_ |
| not modelled | 7.9 | 26 | PDB header:hydrolase Chain: A: PDB Molecule:chitinase a; PDBTitle: crystal structure of inactive mutant e315m chitinase a from2 vibrio harveyi
38 | c3b9tD_ |
| not modelled | 7.9 | 40 | PDB header:hydrolase Chain: D: PDB Molecule:twin-arginine translocation pathway signal protein; PDBTitle: crystal structure of predicted acetamidase/formamidase (yp_546212.1)2 from methylobacillus flagellatus kt at 1.58 a resolution
39 | c2zu8A_ |
| not modelled | 7.6 | 47 | PDB header:transferase Chain: A: PDB Molecule:mannosyl-3-phosphoglycerate synthase; PDBTitle: crystal structure of mannosyl-3-phosphoglycerate synthase2 from pyrococcus horikoshii
40 | c3pssB_ |
| not modelled | 7.6 | 17 | PDB header:cell cycle Chain: B: PDB Molecule:qnr; PDBTitle: crystal structure of ahqnr, the qnr protein from aeromonas hydrophila2 (p21 crystal form)
41 | c2eg9B_ |
| not modelled | 7.1 | 26 | PDB header:hydrolase Chain: B: PDB Molecule:adp-ribosyl cyclase 1; PDBTitle: crystal structure of the truncated extracellular domain of2 mouse cd38
42 | d2cqka1 |
| not modelled | 7.1 | 15 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:"Winged helix" DNA-binding domain Family:La domain
43 | d1xnta_ |
| not modelled | 6.9 | 27 | Fold:Galactose-binding domain-like Superfamily:Galactose-binding domain-like Family:N-terminal domain of xrcc1
44 | c1xnaA_ |
| not modelled | 6.9 | 27 | PDB header:dna binding protein Chain: A: PDB Molecule:protein (dna-repair protein xrcc1); PDBTitle: nmr solution structure of the single-strand break repair2 protein xrcc1-n-terminal domain
45 | d1sura_ |
| not modelled | 6.8 | 16 | Fold:Adenine nucleotide alpha hydrolase-like Superfamily:Adenine nucleotide alpha hydrolases-like Family:PAPS reductase-like
46 | c3n3fB_ |
| not modelled | 6.7 | 14 | PDB header:protein binding Chain: B: PDB Molecule:collagen alpha-1(xv) chain; PDBTitle: crystal structure of the human collagen xv trimerization domain: a2 potent trimerizing unit common to multiplexin collagens
47 | c2xz2A_ |
| not modelled | 6.6 | 26 | PDB header:rna-binding protein Chain: A: PDB Molecule:cstf-50, isoform b; PDBTitle: crystal structure of cstf-50 homodimerization domain
48 | c2vbeA_ |
| not modelled | 6.6 | 39 | PDB header:viral protein Chain: A: PDB Molecule:tailspike-protein; PDBTitle: tailspike protein of bacteriophage sf6
49 | c3cgiD_ |
| not modelled | 6.4 | 50 | PDB header:unknown function Chain: D: PDB Molecule:propanediol utilization protein pduu; PDBTitle: crystal structure of the pduu shell protein from the pdu2 microcompartment
50 | d1hs5a_ |
| not modelled | 6.4 | 34 | Fold:p53 tetramerization domain Superfamily:p53 tetramerization domain Family:p53 tetramerization domain
51 | c2goyC_ |
| not modelled | 6.4 | 22 | PDB header:oxidoreductase Chain: C: PDB Molecule:adenosine phosphosulfate reductase; PDBTitle: crystal structure of assimilatory adenosine 5'-2 phosphosulfate reductase with bound aps
52 | c1d0rA_ |
| not modelled | 6.3 | 26 | PDB header:hormone/growth factor Chain: A: PDB Molecule:glucagon-like peptide-1-(7-36)-amide; PDBTitle: solution structure of glucagon-like peptide-1-(7-36)-amide2 in trifluoroethanol/water
53 | c2bhlB_ |
| not modelled | 6.3 | 43 | PDB header:oxidoreductase (choh(d)-nadp) Chain: B: PDB Molecule:glucose-6-phosphate 1-dehydrogenase; PDBTitle: x-ray structure of human glucose-6-phosphate dehydrogenase2 (deletion variant) complexed with glucose-6-phosphate
54 | c1yj5B_ |
| not modelled | 6.3 | 20 | PDB header:transferase Chain: B: PDB Molecule:5' polynucleotide kinase-3' phosphatase catalytic domain; PDBTitle: molecular architecture of mammalian polynucleotide kinase, a dna2 repair enzyme
55 | d2a1ja1 |
| not modelled | 6.2 | 17 | Fold:SAM domain-like Superfamily:RuvA domain 2-like Family:Hef domain-like
56 | c3nb2B_ |
| not modelled | 6.1 | 25 | PDB header:ligase Chain: B: PDB Molecule:secreted effector protein; PDBTitle: crystal structure of e. coli o157:h7 effector protein nlel
57 | c2j9wB_ |
| not modelled | 6.1 | 19 | PDB header:protein transport Chain: B: PDB Molecule:vps28-prov protein; PDBTitle: structural insight into the escrt-i-ii link and its role in2 mvb trafficking
58 | d1khia2 |
| not modelled | 6.1 | 36 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Cold shock DNA-binding domain-like
59 | d1whra_ |
| not modelled | 6.0 | 14 | Fold:IF3-like Superfamily:R3H domain Family:R3H domain
60 | d1wvfa1 |
| not modelled | 5.9 | 31 | Fold:Ferredoxin-like Superfamily:FAD-linked oxidases, C-terminal domain Family:Vanillyl-alcohol oxidase-like
61 | d2f4la1 |
| not modelled | 5.8 | 24 | Fold:CUB-like Superfamily:Acetamidase/Formamidase-like Family:Acetamidase/Formamidase-like
62 | c3hugJ_ |
| not modelled | 5.8 | 30 | PDB header:transcription/membrane protein Chain: J: PDB Molecule:probable conserved membrane protein; PDBTitle: crystal structure of mycobacterium tuberculosis anti-sigma factor rsla2 in complex with -35 promoter binding domain of sigl
63 | d1edqa2 |
| not modelled | 5.8 | 25 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Type II chitinase
64 | d2bm5a1 |
| not modelled | 5.7 | 4 | Fold:Single-stranded right-handed beta-helix Superfamily:Pentapeptide repeat-like Family:Pentapeptide repeats
65 | d1mjea2 |
| not modelled | 5.7 | 28 | Fold:BRCA2 tower domain Superfamily:BRCA2 tower domain Family:BRCA2 tower domain
66 | c2c1tA_ |
| not modelled | 5.6 | 17 | PDB header:protein transport/membrane protein Chain: A: PDB Molecule:importin alpha subunit; PDBTitle: structure of the kap60p:nup2 complex
67 | c1qkiE_ |
| not modelled | 5.6 | 43 | PDB header:oxidoreductase Chain: E: PDB Molecule:glucose-6-phosphate 1-dehydrogenase; PDBTitle: x-ray structure of human glucose 6-phosphate dehydrogenase2 (variant canton r459l) complexed with structural nadp+
68 | d1r4pb_ |
| not modelled | 5.5 | 39 | Fold:OB-fold Superfamily:Bacterial enterotoxins Family:Bacterial AB5 toxins, B-subunits
69 | d1l8na1 |
| not modelled | 5.5 | 45 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:alpha-D-glucuronidase/Hyaluronidase catalytic domain
70 | d2ef1a1 |
| not modelled | 5.5 | 23 | Fold:Flavodoxin-like Superfamily:N-(deoxy)ribosyltransferase-like Family:ADP ribosyl cyclase-like
71 | d1c4qa_ |
| not modelled | 5.3 | 33 | Fold:OB-fold Superfamily:Bacterial enterotoxins Family:Bacterial AB5 toxins, B-subunits
72 | d1zs4a1 |
| not modelled | 5.3 | 23 | Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:Bacteriophage CII protein
73 | c2o8vA_ |
| not modelled | 5.2 | 21 | PDB header:oxidoreductase Chain: A: PDB Molecule:phosphoadenosine phosphosulfate reductase; PDBTitle: paps reductase in a covalent complex with thioredoxin c35a

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