Phyre 2 Results for Q47319

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Email | l.a.kelley@imperial.ac.uk
Description | Q47319
Date | Thu Jan 5 12:36:46 GMT 2012
Unique Job ID | 50aacaf3b68994f6

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c1rk8C_
Top template information
PDB header:translation Chain: C: PDB Molecule:within the bgcn gene intron protein; PDBTitle: structure of the cytosolic protein pym bound to the mago-2 y14 core of the exon junction complex
Confidence and coverage
Confidence: | 53.4% | Coverage: | 4%
9 residues ( 4% of your sequence) have been modelled with 53.4% confidence by the single highest scoring template.
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3D viewing
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Sequence analysis |

Secondary structure and disorder prediction |

|  | 1 | . | . | . | . | . | . | . | . | 10 | . | . | . | . | . | . | . | . | . | 20 | . | . | . | . | . | . | . | . | . | 30 | . | . | . | . | . | . | . | . | . | 40 | . | . | . | . | . | . | . | . | . | 50 | . | . | . | . | . | . | . | . | . | 60
Sequence |  | M | T | E | N | A | V | L | Q | L | R | A | E | R | I | A | R | A | T | R | P | F | L | A | R | G | N | R | V | R | R | C | Q | R | C | L | L | P | E | K | L | C | L | C | S | T | I | T | P | A | Q | A | K | S | R | F | C | L | L | M | F
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | D | T | E | P | M | K | P | S | N | T | G | R | L | I | A | D | I | L | P | D | T | V | A | F | Q | W | S | R | T | E | P | S | Q | D | L | L | E | L | V | Q | N | P | D | Y | Q | P | M | V | V | F | P | A | S | Y | A | D | E | Q | R | E
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  | ? | ? |  | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | V | I | F | T | P | P | A | G | K | P | P | L | F | I | M | L | D | G | T | W | P | E | A | R | K | M | F | R | K | S | P | Y | L | D | N | L | P | V | I | S | V | D | L | S | R | L | S | A | Y | R | L | R | E | A | Q | A | E | G | Q | Y
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | .
Sequence |  | C | T | A | E | V | A | I | A | L | L | D | M | A | G | D | T | G | A | A | A | G | L | G | E | H | F | T | R | F | K | T | R | Y | L | A | G | K | T | Q | H | L | G | S | I | T | A | E | Q | L | E | S | V
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 |
| c1rk8C_ |

### PDB 1rk8 chain C

Region: 137 - 145
Aligned: 9
Modelled: 9
Confidence: 53.4%
Identity: 67%
PDB header:translation
Chain: C: PDB Molecule:within the bgcn gene intron protein;
PDBTitle: structure of the cytosolic protein pym bound to the mago-2 y14 core of the exon junction complex

Phyre2
2 |
| d1rk8c_ |

### PDB 1rk8 chain C

Region: 137 - 145
Aligned: 9
Modelled: 9
Confidence: 53.4%
Identity: 67%
Fold: WW domain-like
Superfamily: Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain
Family: Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain

Phyre2
3 |
| d1xrxa1 |

### PDB 1xrx chain A domain 1

Region: 207 - 232
Aligned: 26
Modelled: 25
Confidence: 40.6%
Identity: 23%
Fold: Ribbon-helix-helix
Superfamily: Ribbon-helix-helix
Family: SeqA N-terminal domain-like

Phyre2
4 |
| c1xrxD_ |

### PDB 1xrx chain D

Region: 207 - 232
Aligned: 26
Modelled: 25
Confidence: 40.6%
Identity: 23%
PDB header:replication inhibitor
Chain: D: PDB Molecule:seqa protein;
PDBTitle: crystal structure of a dna-binding protein

Phyre2
5 |
| c3mopC_ |

### PDB 3mop chain C

Region: 181 - 220
Aligned: 40
Modelled: 40
Confidence: 32.1%
Identity: 20%
PDB header:signaling protein, immune system
Chain: C: PDB Molecule:myeloid differentiation primary response protein myd88;
PDBTitle: the ternary death domain complex of myd88, irak4, and irak2

Phyre2
6 |
| c3c6fD_ |

### PDB 3c6f chain D

Region: 97 - 142
Aligned: 46
Modelled: 46
Confidence: 30.7%
Identity: 7%
PDB header:structural genomics, unknown function
Chain: D: PDB Molecule:yetf protein;
PDBTitle: crystal structure of protein bsu07140 from bacillus subtilis

Phyre2
7 |
| d2dofa1 |

### PDB 2dof chain A domain 1

Region: 137 - 159
Aligned: 23
Modelled: 23
Confidence: 22.5%
Identity: 22%
Fold: Another 3-helical bundle
Superfamily: FF domain
Family: FF domain

Phyre2
8 |
| c3bvoA_ |

### PDB 3bvo chain A

Region: 29 - 52
Aligned: 24
Modelled: 24
Confidence: 22.3%
Identity: 29%
PDB header:chaperone
Chain: A: PDB Molecule:co-chaperone protein hscb, mitochondrial precursor;
PDBTitle: crystal structure of human co-chaperone protein hscb

Phyre2
9 |
| d1ffya1 |

### PDB 1ffy chain A domain 1

Region: 26 - 36
Aligned: 11
Modelled: 11
Confidence: 22.2%
Identity: 27%
Fold: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Superfamily: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
Family: Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases

Phyre2
10 |
| d2dara2 |

### PDB 2dar chain A domain 2

Region: 25 - 37
Aligned: 13
Modelled: 13
Confidence: 20.0%
Identity: 31%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: LIM domain

Phyre2
11 |
| d1yuda1 |

### PDB 1yud chain A domain 1

Region: 106 - 143
Aligned: 38
Modelled: 38
Confidence: 18.2%
Identity: 13%
Fold: Double-stranded beta-helix
Superfamily: RmlC-like cupins
Family: YML079-like

Phyre2
12 |
| c3lzzB_ |

### PDB 3lzz chain B

Region: 107 - 141
Aligned: 35
Modelled: 35
Confidence: 15.5%
Identity: 6%
PDB header:unknown function
Chain: B: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structures of cupin superfamily bbduf985 from branchiostoma2 belcheri tsingtauense in apo and gdp-bound forms

Phyre2
13 |
| d1esza_ |

### PDB 1esz chain A

Region: 129 - 159
Aligned: 31
Modelled: 31
Confidence: 15.2%
Identity: 13%
Fold: Chelatase-like
Superfamily: "Helical backbone" metal receptor
Family: Periplasmic ferric siderophore binding protein FhuD

Phyre2
14 |
| d2apob1 |

### PDB 2apo chain B domain 1

Region: 27 - 55
Aligned: 29
Modelled: 27
Confidence: 14.8%
Identity: 28%
Fold: Rubredoxin-like
Superfamily: Nop10-like SnoRNP
Family: Nucleolar RNA-binding protein Nop10-like

Phyre2
15 |
| c2kiqA_ |

### PDB 2kiq chain A

Region: 137 - 157
Aligned: 21
Modelled: 21
Confidence: 14.8%
Identity: 14%
PDB header:transcription regulator
Chain: A: PDB Molecule:transcription elongation regulator 1;
PDBTitle: solution structure of the ff domain 2 of human transcription2 elongation factor ca150

Phyre2
16 |
| c2knqA_ |

### PDB 2knq chain A

Region: 107 - 141
Aligned: 35
Modelled: 35
Confidence: 13.4%
Identity: 20%
PDB header:protein transport
Chain: A: PDB Molecule:general secretion pathway protein h;
PDBTitle: solution structure of e.coli gsph

Phyre2
17 |
| d1ctla1 |

### PDB 1ctl chain A domain 1

Region: 25 - 40
Aligned: 15
Modelled: 16
Confidence: 13.3%
Identity: 27%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: LIM domain

Phyre2
18 |
| d2vkva2 |

### PDB 2vkv chain A domain 2

Region: 137 - 216
Aligned: 75
Modelled: 75
Confidence: 13.3%
Identity: 12%
Fold: Tetracyclin repressor-like, C-terminal domain
Superfamily: Tetracyclin repressor-like, C-terminal domain
Family: Tetracyclin repressor-like, C-terminal domain

Phyre2
19 |
| d1imla1 |

### PDB 1iml chain A domain 1

Region: 29 - 40
Aligned: 12
Modelled: 12
Confidence: 13.1%
Identity: 17%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: LIM domain

Phyre2
20 |
| d1ibia1 |

### PDB 1ibi chain A domain 1

Region: 28 - 35
Aligned: 8
Modelled: 8
Confidence: 12.1%
Identity: 38%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: LIM domain

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | c1rk8C_ |
|  | 53.4 | 67 | PDB header:translation Chain: C: PDB Molecule:within the bgcn gene intron protein; PDBTitle: structure of the cytosolic protein pym bound to the mago-2 y14 core of the exon junction complex
2 | d1rk8c_ |
|  | 53.4 | 67 | Fold:WW domain-like Superfamily:Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain Family:Pym (Within the bgcn gene intron protein, WIBG), N-terminal domain
3 | d1xrxa1 |
|  | 40.6 | 23 | Fold:Ribbon-helix-helix Superfamily:Ribbon-helix-helix Family:SeqA N-terminal domain-like
4 | c1xrxD_ |
|  | 40.6 | 23 | PDB header:replication inhibitor Chain: D: PDB Molecule:seqa protein; PDBTitle: crystal structure of a dna-binding protein
5 | c3mopC_ |
|  | 32.1 | 20 | PDB header:signaling protein, immune system Chain: C: PDB Molecule:myeloid differentiation primary response protein myd88; PDBTitle: the ternary death domain complex of myd88, irak4, and irak2
6 | c3c6fD_ |
|  | 30.7 | 7 | PDB header:structural genomics, unknown function Chain: D: PDB Molecule:yetf protein; PDBTitle: crystal structure of protein bsu07140 from bacillus subtilis
7 | d2dofa1 |
|  | 22.5 | 22 | Fold:Another 3-helical bundle Superfamily:FF domain Family:FF domain
8 | c3bvoA_ |
|  | 22.3 | 29 | PDB header:chaperone Chain: A: PDB Molecule:co-chaperone protein hscb, mitochondrial precursor; PDBTitle: crystal structure of human co-chaperone protein hscb
9 | d1ffya1 |
|  | 22.2 | 27 | Fold:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Superfamily:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases Family:Anticodon-binding domain of a subclass of class I aminoacyl-tRNA synthetases
10 | d2dara2 |
|  | 20.0 | 31 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
11 | d1yuda1 |
|  | 18.2 | 13 | Fold:Double-stranded beta-helix Superfamily:RmlC-like cupins Family:YML079-like
12 | c3lzzB_ |
|  | 15.5 | 6 | PDB header:unknown function Chain: B: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structures of cupin superfamily bbduf985 from branchiostoma2 belcheri tsingtauense in apo and gdp-bound forms
13 | d1esza_ |
|  | 15.2 | 13 | Fold:Chelatase-like Superfamily:"Helical backbone" metal receptor Family:Periplasmic ferric siderophore binding protein FhuD
14 | d2apob1 |
|  | 14.8 | 28 | Fold:Rubredoxin-like Superfamily:Nop10-like SnoRNP Family:Nucleolar RNA-binding protein Nop10-like
15 | c2kiqA_ |
|  | 14.8 | 14 | PDB header:transcription regulator Chain: A: PDB Molecule:transcription elongation regulator 1; PDBTitle: solution structure of the ff domain 2 of human transcription2 elongation factor ca150
16 | c2knqA_ |
|  | 13.4 | 20 | PDB header:protein transport Chain: A: PDB Molecule:general secretion pathway protein h; PDBTitle: solution structure of e.coli gsph
17 | d1ctla1 |
|  | 13.3 | 27 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
18 | d2vkva2 |
|  | 13.3 | 12 | Fold:Tetracyclin repressor-like, C-terminal domain Superfamily:Tetracyclin repressor-like, C-terminal domain Family:Tetracyclin repressor-like, C-terminal domain
19 | d1imla1 |
|  | 13.1 | 17 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
20 | d1ibia1 |
|  | 12.1 | 38 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
21 | c2elpA_ |
| not modelled | 11.8 | 20 | PDB header:transcription Chain: A: PDB Molecule:zinc finger protein 406; PDBTitle: solution structure of the 13th c2h2 zinc finger of human2 zinc finger protein 406
22 | c2a7yA_ |
| not modelled | 11.6 | 25 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein rv2302/mt2359; PDBTitle: solution structure of the conserved hypothetical protein2 rv2302 from the bacterium mycobacterium tuberculosis
23 | d2a7ya1 |
| not modelled | 11.6 | 25 | Fold:SH3-like barrel Superfamily:Cell growth inhibitor/plasmid maintenance toxic component Family:Rv2302-like
24 | d2etva1 |
| not modelled | 11.2 | 6 | Fold:Chelatase-like Superfamily:"Helical backbone" metal receptor Family:TM0189-like
25 | d2ey4e1 |
| not modelled | 10.4 | 31 | Fold:Rubredoxin-like Superfamily:Nop10-like SnoRNP Family:Nucleolar RNA-binding protein Nop10-like
26 | c2yetB_ |
| not modelled | 10.2 | 18 | PDB header:hydrolase Chain: B: PDB Molecule:gh61 isozyme a; PDBTitle: thermoascus gh61 isozyme a
27 | c2nrrA_ |
| not modelled | 10.0 | 20 | PDB header:hydrolase Chain: A: PDB Molecule:uvrabc system protein c; PDBTitle: crystal structure of the c-terminal rnaseh endonuclase2 domain of uvrc
28 | c2kfdA_ |
| not modelled | 10.0 | 32 | PDB header:nuclear protein Chain: A: PDB Molecule:pre-mrna-processing protein prp40; PDBTitle: prp40 ff4 domain
29 | d1v95a_ |
| not modelled | 9.7 | 8 | Fold:Anticodon-binding domain-like Superfamily:Class II aaRS ABD-related Family:Anticodon-binding domain of Class II aaRS
30 | d2afaa1 |
| not modelled | 9.5 | 7 | Fold:alpha/alpha toroid Superfamily:Six-hairpin glycosidases Family:N-acylglucosamine (NAG) epimerase
31 | d1zbdb_ |
| not modelled | 9.1 | 19 | Fold:FYVE/PHD zinc finger Superfamily:FYVE/PHD zinc finger Family:FYVE, a phosphatidylinositol-3-phosphate binding domain
32 | c2iy3A_ |
| not modelled | 9.0 | 11 | PDB header:rna-binding Chain: A: PDB Molecule:signal recognition particle protein ffh; PDBTitle: structure of the e. coli signal recognition particle2 bound to a translating ribosome
33 | c2rr7A_ |
| not modelled | 8.9 | 36 | PDB header:motor protein Chain: A: PDB Molecule:dynein heavy chain 9; PDBTitle: microtubule binding domain of dynein-c
34 | d2ewoa1 |
| not modelled | 8.8 | 12 | Fold:Pentein, beta/alpha-propeller Superfamily:Pentein Family:Porphyromonas-type peptidylarginine deiminase
35 | c3n43B_ |
| not modelled | 8.6 | 58 | PDB header:viral protein Chain: B: PDB Molecule:e2 envelope glycoprotein; PDBTitle: crystal structures of the mature envelope glycoprotein complex2 (trypsin cleavage) of chikungunya virus.
36 | c2hw4A_ |
| not modelled | 8.5 | 21 | PDB header:structural genomics, hydrolase Chain: A: PDB Molecule:14 kda phosphohistidine phosphatase; PDBTitle: crystal structure of human phosphohistidine phosphatase
37 | d2cu8a1 |
| not modelled | 8.4 | 20 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
38 | c2xfbI_ |
| not modelled | 8.4 | 58 | PDB header:virus Chain: I: PDB Molecule:e2 envelope glycoprotein; PDBTitle: the chikungunya e1 e2 envelope glycoprotein complex fit into2 the sindbis virus cryo-em map
39 | c3mhsE_ |
| not modelled | 8.4 | 40 | PDB header:hydrolase/transcription regulator/protei Chain: E: PDB Molecule:saga-associated factor 73; PDBTitle: structure of the saga ubp8/sgf11/sus1/sgf73 dub module bound to2 ubiquitin aldehyde
40 | d1lf6a2 |
| not modelled | 8.3 | 23 | Fold:Supersandwich Superfamily:Galactose mutarotase-like Family:Bacterial glucoamylase N-terminal domain-like
41 | c2k85A_ |
| not modelled | 8.2 | 16 | PDB header:protein binding Chain: A: PDB Molecule:glucocorticoid receptor dna-binding factor 1; PDBTitle: p190-a rhogap ff1 domain
42 | c2iv0A_ |
| not modelled | 8.2 | 9 | PDB header:oxidoreductase Chain: A: PDB Molecule:isocitrate dehydrogenase; PDBTitle: thermal stability of isocitrate dehydrogenase from2 archaeoglobus fulgidus studied by crystal structure3 analysis and engineering of chimers
43 | c2hfvA_ |
| not modelled | 8.0 | 16 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein rpa1041; PDBTitle: solution nmr structure of protein rpa1041 from pseudomonas2 aeruginosa. northeast structural genomics consortium3 target pat90.
44 | c1qu2A_ |
| not modelled | 7.8 | 27 | PDB header:ligase/rna Chain: A: PDB Molecule:isoleucyl-trna synthetase; PDBTitle: insights into editing from an ile-trna synthetase structure2 with trna(ile) and mupirocin
45 | d1xo1a2 |
| not modelled | 7.6 | 27 | Fold:PIN domain-like Superfamily:PIN domain-like Family:5' to 3' exonuclease catalytic domain
46 | d1ulva4 |
| not modelled | 7.6 | 25 | Fold:Supersandwich Superfamily:Galactose mutarotase-like Family:Bacterial glucoamylase N-terminal domain-like
47 | c3errB_ |
| not modelled | 7.4 | 10 | PDB header:ligase Chain: B: PDB Molecule:fusion protein of microtubule binding domain from PDBTitle: microtubule binding domain from mouse cytoplasmic dynein as2 a fusion with seryl-trna synthetase
48 | d1kl7a_ |
| not modelled | 7.4 | 12 | Fold:Tryptophan synthase beta subunit-like PLP-dependent enzymes Superfamily:Tryptophan synthase beta subunit-like PLP-dependent enzymes Family:Tryptophan synthase beta subunit-like PLP-dependent enzymes
49 | c3muwU_ |
| not modelled | 7.1 | 42 | PDB header:virus Chain: U: PDB Molecule:structural polyprotein; PDBTitle: pseudo-atomic structure of the e2-e1 protein shell in sindbis virus
50 | d2doea1 |
| not modelled | 6.9 | 10 | Fold:Another 3-helical bundle Superfamily:FF domain Family:FF domain
51 | c2ofqA_ |
| not modelled | 6.9 | 14 | PDB header:protein transport/protein transport Chain: A: PDB Molecule:trao; PDBTitle: nmr solution structure of a complex between the virb9/virb72 interaction domains of the pkm101 type iv secretion system
52 | d1ryqa_ |
| not modelled | 6.9 | 15 | Fold:Rubredoxin-like Superfamily:RNA polymerase subunits Family:RpoE2-like
53 | c3k7bA_ |
| not modelled | 6.7 | 40 | PDB header:viral protein Chain: A: PDB Molecule:protein a33; PDBTitle: the structure of the poxvirus a33 protein reveals a dimer of unique c-2 type lectin-like domains.
54 | c3kepA_ |
| not modelled | 6.7 | 15 | PDB header:protein transport, rna binding protein Chain: A: PDB Molecule:nucleoporin nup145; PDBTitle: crystal structure of the autoproteolytic domain from the2 nuclear pore complex component nup145 from saccharomyces3 cerevisiae
55 | d1pn0a2 |
| not modelled | 6.6 | 8 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like
56 | c3chxG_ |
| not modelled | 6.5 | 67 | PDB header:membrane protein Chain: G: PDB Molecule:pmoc; PDBTitle: crystal structure of methylosinus trichosporium ob3b2 particulate methane monooxygenase (pmmo)
57 | c3n40P_ |
| not modelled | 6.5 | 58 | PDB header:viral protein Chain: P: PDB Molecule:p62 envelope glycoprotein; PDBTitle: crystal structure of the immature envelope glycoprotein complex of2 chikungunya virus.
58 | c2jyvA_ |
| not modelled | 6.2 | 57 | PDB header:cytokine Chain: A: PDB Molecule:granulin-2; PDBTitle: human granulin f
59 | d1omza_ |
| not modelled | 6.1 | 11 | Fold:Nucleotide-diphospho-sugar transferases Superfamily:Nucleotide-diphospho-sugar transferases Family:Exostosin
60 | d2hfva1 |
| not modelled | 6.0 | 16 | Fold:Ferredoxin-like Superfamily:GlnB-like Family:RPA1041-like
61 | d1bpoa1 |
| not modelled | 6.0 | 20 | Fold:alpha-alpha superhelix Superfamily:ARM repeat Family:Clathrin heavy-chain linker domain
62 | c1yewC_ |
| not modelled | 5.9 | 57 | PDB header:oxidoreductase, membrane protein Chain: C: PDB Molecule:particulate methane monooxygenase subunit c2; PDBTitle: crystal structure of particulate methane monooxygenase
63 | c3g9yA_ |
| not modelled | 5.9 | 29 | PDB header:transcription/rna Chain: A: PDB Molecule:zinc finger ran-binding domain-containing protein 2; PDBTitle: crystal structure of the second zinc finger from zranb2/znf265 bound2 to 6 nt ssrna sequence agguaa
64 | d2gnra1 |
| not modelled | 5.8 | 29 | Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:SSO2064-like
65 | c2xzn5_ |
| not modelled | 5.7 | 36 | PDB header:ribosome Chain: 5: PDB Molecule:ribosomal protein s26e containing protein; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2
66 | d2cqna1 |
| not modelled | 5.7 | 29 | Fold:Another 3-helical bundle Superfamily:FF domain Family:FF domain
67 | c2nvuB_ |
| not modelled | 5.6 | 29 | PDB header:protein turnover, ligase Chain: B: PDB Molecule:maltose binding protein/nedd8-activating enzyme PDBTitle: structure of appbp1-uba3~nedd8-nedd8-mgatp-ubc12(c111a), a2 trapped ubiquitin-like protein activation complex
68 | d1j3kc_ |
| not modelled | 5.5 | 7 | Fold:Thymidylate synthase/dCMP hydroxymethylase Superfamily:Thymidylate synthase/dCMP hydroxymethylase Family:Thymidylate synthase/dCMP hydroxymethylase
69 | d3blza1 |
| not modelled | 5.3 | 20 | Fold:Cystatin-like Superfamily:NTF2-like Family:Sbal0622-like
70 | c3eabD_ |
| not modelled | 5.3 | 23 | PDB header:cell cycle Chain: D: PDB Molecule:spastin; PDBTitle: crystal structure of spastin mit in complex with escrt iii
71 | c1ko6A_ |
| not modelled | 5.3 | 18 | PDB header:transferase Chain: A: PDB Molecule:nuclear pore complex protein nup98; PDBTitle: crystal structure of c-terminal autoproteolytic domain of2 nucleoporin nup98
72 | d1aa7a_ |
| not modelled | 5.1 | 26 | Fold:Influenza virus matrix protein M1 Superfamily:Influenza virus matrix protein M1 Family:Influenza virus matrix protein M1
73 | d1vkpa_ |
| not modelled | 5.1 | 17 | Fold:Pentein, beta/alpha-propeller Superfamily:Pentein Family:Porphyromonas-type peptidylarginine deiminase

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