Phyre 2 Results for P30745

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Email | l.a.kelley@imperial.ac.uk
Description | P30745
Date | Thu Jan 5 11:46:21 GMT 2012
Unique Job ID | 58c6133f13623dbd

Summary |

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

Model (left) based on template d1tv8a_
Top template information
Fold:TIM beta/alpha-barrel Superfamily:Radical SAM enzymes Family:MoCo biosynthesis proteins
Confidence and coverage
Confidence: | 100.0% | Coverage: | 94%
308 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 | A | S | Q | L | T | D | A | F | A | R | K | F | Y | Y | L | R | L | S | I | T | D | V | C | N | F | R | C | T | Y | C | L | P | D | G | Y | K | P | S | G | V | T | N | K | G | F | L | T | V | D | E | I | R | R | V | T | R | A | F | A
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | . | . | 90 | . | . | . | . | . | . | . | . | . | 100 | . | . | . | . | . | . | . | . | . | 110 | . | . | . | . | . | . | . | . | . | 120
Sequence |  | R | L | G | T | E | K | V | R | L | T | G | G | E | P | S | L | R | R | D | F | T | D | I | I | A | A | V | R | E | N | D | A | I | R | Q | I | A | V | T | T | N | G | Y | R | L | E | R | D | V | A | S | W | R | D | A | G | L | T | G | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 130 | . | . | . | . | . | . | . | . | . | 140 | . | . | . | . | . | . | . | . | . | 150 | . | . | . | . | . | . | . | . | . | 160 | . | . | . | . | . | . | . | . | . | 170 | . | . | . | . | . | . | . | . | . | 180
Sequence |  | N | V | S | V | D | S | L | D | A | R | Q | F | H | A | I | T | G | Q | D | K | F | N | Q | V | M | A | G | I | D | A | A | F | E | A | G | F | E | K | V | K | V | N | T | V | L | M | R | D | V | N | H | H | Q | L | D | T | F | L | N | W
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 190 | . | . | . | . | . | . | . | . | . | 200 | . | . | . | . | . | . | . | . | . | 210 | . | . | . | . | . | . | . | . | . | 220 | . | . | . | . | . | . | . | . | . | 230 | . | . | . | . | . | . | . | . | . | 240
Sequence |  | I | Q | H | R | P | I | Q | L | R | F | I | E | L | M | E | T | G | E | G | S | E | L | F | R | K | H | H | I | S | G | Q | V | L | R | D | E | L | L | R | R | G | W | I | H | Q | L | R | Q | R | S | D | G | P | A | Q | V | F | C | H | P
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? |  | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 250 | . | . | . | . | . | . | . | . | . | 260 | . | . | . | . | . | . | . | . | . | 270 | . | . | . | . | . | . | . | . | . | 280 | . | . | . | . | . | . | . | . | . | 290 | . | . | . | . | . | . | . | . | . | 300
Sequence |  | D | Y | A | G | E | I | G | L | I | M | P | Y | E | K | D | F | C | A | T | C | N | R | L | R | V | S | S | I | G | K | L | H | L | C | L | F | G | E | G | G | V | N | L | R | D | L | L | E | D | D | T | Q | Q | Q | A | L | E | A | R | I
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? |  | ? |  |  |  |  |  |  |  | ? |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 310 | . | . | . | . | . | . | . | . | . | 320 | . | . | . | . | . | . | . | . | .
Sequence |  | S | A | A | L | R | E | K | K | Q | T | H | F | L | H | Q | N | N | T | G | I | T | Q | N | L | S | Y | I | G | G
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 |
| d1tv8a_ |

### PDB 1tv8 chain A

Region: 3 - 311
Aligned: 308
Modelled: 309
Confidence: 100.0%
Identity: 32%
Fold: TIM beta/alpha-barrel
Superfamily: Radical SAM enzymes
Family: MoCo biosynthesis proteins

Phyre2
2 |
| c2yx0A_ |

### PDB 2yx0 chain A

Region: 18 - 228
Aligned: 205
Modelled: 207
Confidence: 99.9%
Identity: 16%
PDB header:metal binding protein
Chain: A: PDB Molecule:radical sam enzyme;
PDBTitle: crystal structure of p. horikoshii tyw1

Phyre2
3 |
| c3c8fA_ |

### PDB 3c8f chain A

Region: 9 - 222
Aligned: 210
Modelled: 213
Confidence: 99.8%
Identity: 12%
PDB header:oxidoreductase
Chain: A: PDB Molecule:pyruvate formate-lyase 1-activating enzyme;
PDBTitle: 4fe-4s-pyruvate formate-lyase activating enzyme with2 partially disordered adomet

Phyre2
4 |
| c1r30A_ |

### PDB 1r30 chain A

Region: 15 - 218
Aligned: 201
Modelled: 204
Confidence: 99.8%
Identity: 17%
PDB header:transferase
Chain: A: PDB Molecule:biotin synthase;
PDBTitle: the crystal structure of biotin synthase, an s-2 adenosylmethionine-dependent radical enzyme

Phyre2
5 |
| d1r30a_ |

### PDB 1r30 chain A

Region: 15 - 218
Aligned: 201
Modelled: 204
Confidence: 99.8%
Identity: 17%
Fold: TIM beta/alpha-barrel
Superfamily: Radical SAM enzymes
Family: Biotin synthase

Phyre2
6 |
| c3t7vA_ |

### PDB 3t7v chain A

Region: 9 - 218
Aligned: 206
Modelled: 210
Confidence: 99.8%
Identity: 14%
PDB header:transferase
Chain: A: PDB Molecule:methylornithine synthase pylb;
PDBTitle: crystal structure of methylornithine synthase (pylb)

Phyre2
7 |
| c2a5hC_ |

### PDB 2a5h chain C

Region: 3 - 272
Aligned: 249
Modelled: 270
Confidence: 99.8%
Identity: 18%
PDB header:isomerase
Chain: C: PDB Molecule:l-lysine 2,3-aminomutase;
PDBTitle: 2.1 angstrom x-ray crystal structure of lysine-2,3-aminomutase from2 clostridium subterminale sb4, with michaelis analog (l-alpha-lysine3 external aldimine form of pyridoxal-5'-phosphate).

Phyre2
8 |
| c3cixA_ |

### PDB 3cix chain A

Region: 9 - 218
Aligned: 206
Modelled: 210
Confidence: 99.7%
Identity: 14%
PDB header:adomet binding protein
Chain: A: PDB Molecule:fefe-hydrogenase maturase;
PDBTitle: x-ray structure of the [fefe]-hydrogenase maturase hyde from2 thermotoga maritima in complex with thiocyanate

Phyre2
9 |
| c3rfaA_ |

### PDB 3rfa chain A

Region: 15 - 221
Aligned: 201
Modelled: 207
Confidence: 99.7%
Identity: 17%
PDB header:oxidoreductase
Chain: A: PDB Molecule:ribosomal rna large subunit methyltransferase n;
PDBTitle: x-ray structure of rlmn from escherichia coli in complex with s-2 adenosylmethionine

Phyre2
10 |
| c2z2uA_ |

### PDB 2z2u chain A

Region: 24 - 243
Aligned: 202
Modelled: 207
Confidence: 99.5%
Identity: 15%
PDB header:metal binding protein
Chain: A: PDB Molecule:upf0026 protein mj0257;
PDBTitle: crystal structure of archaeal tyw1

Phyre2
11 |
| d1olta_ |

### PDB 1olt chain A

Region: 3 - 206
Aligned: 203
Modelled: 204
Confidence: 99.5%
Identity: 13%
Fold: TIM beta/alpha-barrel
Superfamily: Radical SAM enzymes
Family: Oxygen-independent coproporphyrinogen III oxidase HemN

Phyre2
12 |
| c3canA_ |

### PDB 3can chain A

Region: 67 - 222
Aligned: 149
Modelled: 156
Confidence: 99.5%
Identity: 17%
PDB header:lyase activator
Chain: A: PDB Molecule:pyruvate-formate lyase-activating enzyme;
PDBTitle: crystal structure of a domain of pyruvate-formate lyase-activating2 enzyme from bacteroides vulgatus atcc 8482

Phyre2
13 |
| c2qgqF_ |

### PDB 2qgq chain F

Region: 28 - 221
Aligned: 190
Modelled: 194
Confidence: 99.1%
Identity: 9%
PDB header:structural genomics, unknown function
Chain: F: PDB Molecule:protein tm_1862;
PDBTitle: crystal structure of tm_1862 from thermotoga maritima.2 northeast structural genomics consortium target vr77

Phyre2
14 |
| c3ivuB_ |

### PDB 3ivu chain B

Region: 43 - 192
Aligned: 145
Modelled: 150
Confidence: 97.4%
Identity: 12%
PDB header:transferase
Chain: B: PDB Molecule:homocitrate synthase, mitochondrial;
PDBTitle: homocitrate synthase lys4 bound to 2-og

Phyre2
15 |
| c3eegB_ |

### PDB 3eeg chain B

Region: 42 - 192
Aligned: 148
Modelled: 151
Confidence: 95.6%
Identity: 14%
PDB header:transferase
Chain: B: PDB Molecule:2-isopropylmalate synthase;
PDBTitle: crystal structure of a 2-isopropylmalate synthase from2 cytophaga hutchinsonii

Phyre2
16 |
| c3ewbX_ |

### PDB 3ewb chain X

Region: 38 - 192
Aligned: 152
Modelled: 155
Confidence: 95.0%
Identity: 9%
PDB header:transferase
Chain: X: PDB Molecule:2-isopropylmalate synthase;
PDBTitle: crystal structure of n-terminal domain of putative 2-2 isopropylmalate synthase from listeria monocytogenes

Phyre2
17 |
| c2ftpA_ |

### PDB 2ftp chain A

Region: 43 - 192
Aligned: 149
Modelled: 150
Confidence: 92.7%
Identity: 13%
PDB header:lyase
Chain: A: PDB Molecule:hydroxymethylglutaryl-coa lyase;
PDBTitle: crystal structure of hydroxymethylglutaryl-coa lyase from pseudomonas2 aeruginosa

Phyre2
18 |
| c1nvmG_ |

### PDB 1nvm chain G

Region: 44 - 192
Aligned: 136
Modelled: 137
Confidence: 91.6%
Identity: 15%
PDB header:lyase/oxidoreductase
Chain: G: PDB Molecule:4-hydroxy-2-oxovalerate aldolase;
PDBTitle: crystal structure of a bifunctional aldolase-dehydrogenase :2 sequestering a reactive and volatile intermediate

Phyre2
19 |
| c2cw6B_ |

### PDB 2cw6 chain B

Region: 44 - 192
Aligned: 148
Modelled: 149
Confidence: 90.9%
Identity: 9%
PDB header:lyase
Chain: B: PDB Molecule:hydroxymethylglutaryl-coa lyase, mitochondrial;
PDBTitle: crystal structure of human hmg-coa lyase: insights into2 catalysis and the molecular basis for3 hydroxymethylglutaric aciduria

Phyre2
20 |
| c3bleA_ |

### PDB 3ble chain A

Region: 44 - 192
Aligned: 147
Modelled: 149
Confidence: 90.0%
Identity: 13%
PDB header:transferase
Chain: A: PDB Molecule:citramalate synthase from leptospira interrogans;
PDBTitle: crystal structure of the catalytic domain of licms in2 complexed with malonate

Phyre2
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Detailed template information |

# | Template | Alignment Coverage | 3D Model | Confidence | % i.d. | Template Information
--- | --- | --- | --- | --- | --- | ---
1 | d1tv8a_ |
|  | 100.0 | 32 | Fold:TIM beta/alpha-barrel Superfamily:Radical SAM enzymes Family:MoCo biosynthesis proteins
2 | c2yx0A_ |
|  | 99.9 | 16 | PDB header:metal binding protein Chain: A: PDB Molecule:radical sam enzyme; PDBTitle: crystal structure of p. horikoshii tyw1
3 | c3c8fA_ |
|  | 99.8 | 12 | PDB header:oxidoreductase Chain: A: PDB Molecule:pyruvate formate-lyase 1-activating enzyme; PDBTitle: 4fe-4s-pyruvate formate-lyase activating enzyme with2 partially disordered adomet
4 | c1r30A_ |
|  | 99.8 | 17 | PDB header:transferase Chain: A: PDB Molecule:biotin synthase; PDBTitle: the crystal structure of biotin synthase, an s-2 adenosylmethionine-dependent radical enzyme
5 | d1r30a_ |
|  | 99.8 | 17 | Fold:TIM beta/alpha-barrel Superfamily:Radical SAM enzymes Family:Biotin synthase
6 | c3t7vA_ |
|  | 99.8 | 14 | PDB header:transferase Chain: A: PDB Molecule:methylornithine synthase pylb; PDBTitle: crystal structure of methylornithine synthase (pylb)
7 | c2a5hC_ |
|  | 99.8 | 18 | PDB header:isomerase Chain: C: PDB Molecule:l-lysine 2,3-aminomutase; PDBTitle: 2.1 angstrom x-ray crystal structure of lysine-2,3-aminomutase from2 clostridium subterminale sb4, with michaelis analog (l-alpha-lysine3 external aldimine form of pyridoxal-5'-phosphate).
8 | c3cixA_ |
|  | 99.7 | 14 | PDB header:adomet binding protein Chain: A: PDB Molecule:fefe-hydrogenase maturase; PDBTitle: x-ray structure of the [fefe]-hydrogenase maturase hyde from2 thermotoga maritima in complex with thiocyanate
9 | c3rfaA_ |
|  | 99.7 | 17 | PDB header:oxidoreductase Chain: A: PDB Molecule:ribosomal rna large subunit methyltransferase n; PDBTitle: x-ray structure of rlmn from escherichia coli in complex with s-2 adenosylmethionine
10 | c2z2uA_ |
|  | 99.5 | 15 | PDB header:metal binding protein Chain: A: PDB Molecule:upf0026 protein mj0257; PDBTitle: crystal structure of archaeal tyw1
11 | d1olta_ |
|  | 99.5 | 13 | Fold:TIM beta/alpha-barrel Superfamily:Radical SAM enzymes Family:Oxygen-independent coproporphyrinogen III oxidase HemN
12 | c3canA_ |
|  | 99.5 | 17 | PDB header:lyase activator Chain: A: PDB Molecule:pyruvate-formate lyase-activating enzyme; PDBTitle: crystal structure of a domain of pyruvate-formate lyase-activating2 enzyme from bacteroides vulgatus atcc 8482
13 | c2qgqF_ |
|  | 99.1 | 9 | PDB header:structural genomics, unknown function Chain: F: PDB Molecule:protein tm_1862; PDBTitle: crystal structure of tm_1862 from thermotoga maritima.2 northeast structural genomics consortium target vr77
14 | c3ivuB_ |
|  | 97.4 | 12 | PDB header:transferase Chain: B: PDB Molecule:homocitrate synthase, mitochondrial; PDBTitle: homocitrate synthase lys4 bound to 2-og
15 | c3eegB_ |
|  | 95.6 | 14 | PDB header:transferase Chain: B: PDB Molecule:2-isopropylmalate synthase; PDBTitle: crystal structure of a 2-isopropylmalate synthase from2 cytophaga hutchinsonii
16 | c3ewbX_ |
|  | 95.0 | 9 | PDB header:transferase Chain: X: PDB Molecule:2-isopropylmalate synthase; PDBTitle: crystal structure of n-terminal domain of putative 2-2 isopropylmalate synthase from listeria monocytogenes
17 | c2ftpA_ |
|  | 92.7 | 13 | PDB header:lyase Chain: A: PDB Molecule:hydroxymethylglutaryl-coa lyase; PDBTitle: crystal structure of hydroxymethylglutaryl-coa lyase from pseudomonas2 aeruginosa
18 | c1nvmG_ |
|  | 91.6 | 15 | PDB header:lyase/oxidoreductase Chain: G: PDB Molecule:4-hydroxy-2-oxovalerate aldolase; PDBTitle: crystal structure of a bifunctional aldolase-dehydrogenase :2 sequestering a reactive and volatile intermediate
19 | c2cw6B_ |
|  | 90.9 | 9 | PDB header:lyase Chain: B: PDB Molecule:hydroxymethylglutaryl-coa lyase, mitochondrial; PDBTitle: crystal structure of human hmg-coa lyase: insights into2 catalysis and the molecular basis for3 hydroxymethylglutaric aciduria
20 | c3bleA_ |
|  | 90.0 | 13 | PDB header:transferase Chain: A: PDB Molecule:citramalate synthase from leptospira interrogans; PDBTitle: crystal structure of the catalytic domain of licms in2 complexed with malonate
21 | d1nvma2 |
| not modelled | 89.8 | 14 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:HMGL-like
22 | c1ydnA_ |
| not modelled | 89.5 | 10 | PDB header:lyase Chain: A: PDB Molecule:hydroxymethylglutaryl-coa lyase; PDBTitle: crystal structure of the hmg-coa lyase from brucella melitensis,2 northeast structural genomics target lr35.
23 | c1ydoC_ |
| not modelled | 87.8 | 12 | PDB header:lyase Chain: C: PDB Molecule:hmg-coa lyase; PDBTitle: crystal structure of the bacillis subtilis hmg-coa lyase, northeast2 structural genomics target sr181.
24 | c1sr9A_ |
| not modelled | 82.2 | 10 | PDB header:transferase Chain: A: PDB Molecule:2-isopropylmalate synthase; PDBTitle: crystal structure of leua from mycobacterium tuberculosis
25 | c2nx9B_ |
| not modelled | 82.1 | 12 | PDB header:lyase Chain: B: PDB Molecule:oxaloacetate decarboxylase 2, subunit alpha; PDBTitle: crystal structure of the carboxyltransferase domain of the2 oxaloacetate decarboxylase na+ pump from vibrio cholerae
26 | d1qt1a_ |
| not modelled | 81.1 | 14 | Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:Xylose isomerase
27 | c3khdC_ |
| not modelled | 79.4 | 11 | PDB header:transferase Chain: C: PDB Molecule:pyruvate kinase; PDBTitle: crystal structure of pff1300w.
28 | c2wcsA_ |
| not modelled | 75.4 | 13 | PDB header:hydrolase Chain: A: PDB Molecule:alpha amylase, catalytic region; PDBTitle: crystal structure of debranching enzyme from nostoc2 punctiforme (npde)
29 | d1qhoa4 |
| not modelled | 74.1 | 15 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
30 | c2zyfA_ |
| not modelled | 70.8 | 12 | PDB header:transferase Chain: A: PDB Molecule:homocitrate synthase; PDBTitle: crystal structure of homocitrate synthase from thermus thermophilus2 complexed with magnesuim ion and alpha-ketoglutarate
31 | d2aaaa2 |
| not modelled | 70.7 | 14 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
32 | d1muwa_ |
| not modelled | 68.9 | 17 | Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:Xylose isomerase
33 | d3bmva4 |
| not modelled | 68.5 | 13 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
34 | c1lwhA_ |
| not modelled | 67.6 | 17 | PDB header:transferase Chain: A: PDB Molecule:4-alpha-glucanotransferase; PDBTitle: crystal structure of t. maritima 4-alpha-glucanotransferase
35 | d1pama4 |
| not modelled | 66.7 | 10 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
36 | c1m53A_ |
| not modelled | 66.5 | 13 | PDB header:isomerase Chain: A: PDB Molecule:isomaltulose synthase; PDBTitle: crystal structure of isomaltulose synthase (pali) from2 klebsiella sp. lx3
37 | c3hpxB_ |
| not modelled | 65.3 | 13 | PDB header:transferase Chain: B: PDB Molecule:2-isopropylmalate synthase; PDBTitle: crystal structure of mycobacterium tuberculosis leua active site2 domain 1-425 (truncation mutant delta:426-644)
38 | c3a47A_ |
| not modelled | 64.6 | 9 | PDB header:hydrolase Chain: A: PDB Molecule:oligo-1,6-glucosidase; PDBTitle: crystal structure of isomaltase from saccharomyces cerevisiae
39 | d1cgta4 |
| not modelled | 64.0 | 9 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
40 | d1bf2a3 |
| not modelled | 64.0 | 18 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
41 | d1h3ga3 |
| not modelled | 63.7 | 11 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
42 | d1gjwa2 |
| not modelled | 63.0 | 14 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
43 | d1uoka2 |
| not modelled | 61.5 | 19 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
44 | d1cxla4 |
| not modelled | 58.4 | 9 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
45 | c1ea9D_ |
| not modelled | 58.0 | 13 | PDB header:hydrolase Chain: D: PDB Molecule:cyclomaltodextrinase; PDBTitle: cyclomaltodextrinase
46 | d1m53a2 |
| not modelled | 57.5 | 16 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
47 | c2aaaA_ |
| not modelled | 56.5 | 10 | PDB header:glycosidase Chain: A: PDB Molecule:alpha-amylase; PDBTitle: calcium binding in alpha-amylases: an x-ray diffraction2 study at 2.1 angstroms resolution of two enzymes from3 aspergillus
48 | d1gvia3 |
| not modelled | 56.1 | 10 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
49 | c1uokA_ |
| not modelled | 55.7 | 16 | PDB header:glucosidase Chain: A: PDB Molecule:oligo-1,6-glucosidase; PDBTitle: crystal structure of b. cereus oligo-1,6-glucosidase
50 | d2guya2 |
| not modelled | 54.6 | 11 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
51 | d1e43a2 |
| not modelled | 53.6 | 11 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
52 | c1qhoA_ |
| not modelled | 52.3 | 17 | PDB header:hydrolase Chain: A: PDB Molecule:alpha-amylase; PDBTitle: five-domain alpha-amylase from bacillus stearothermophilus,2 maltose/acarbose complex
53 | d1g5aa2 |
| not modelled | 52.2 | 12 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
54 | d1lwha2 |
| not modelled | 50.7 | 16 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
55 | c2ze0A_ |
| not modelled | 50.0 | 16 | PDB header:hydrolase Chain: A: PDB Molecule:alpha-glucosidase; PDBTitle: alpha-glucosidase gsj
56 | c2zidA_ |
| not modelled | 49.7 | 16 | PDB header:hydrolase Chain: A: PDB Molecule:dextran glucosidase; PDBTitle: crystal structure of dextran glucosidase e236q complex with2 isomaltotriose
57 | c3edeB_ |
| not modelled | 49.7 | 14 | PDB header:hydrolase Chain: B: PDB Molecule:cyclomaltodextrinase; PDBTitle: structural base for cyclodextrin hydrolysis
58 | c1bf2A_ |
| not modelled | 48.9 | 10 | PDB header:hydrolase Chain: A: PDB Molecule:isoamylase; PDBTitle: structure of pseudomonas isoamylase
59 | c2ya0A_ |
| not modelled | 48.7 | 16 | PDB header:hydrolase Chain: A: PDB Molecule:putative alkaline amylopullulanase; PDBTitle: catalytic module of the multi-modular glycogen-degrading2 pneumococcal virulence factor spua
60 | d1ob0a2 |
| not modelled | 48.6 | 14 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
61 | c3dxiB_ |
| not modelled | 48.6 | 9 | PDB header:structural genomics, unknown function Chain: B: PDB Molecule:putative aldolase; PDBTitle: crystal structure of the n-terminal domain of a putative2 aldolase (bvu_2661) from bacteroides vulgatus
62 | c1gjuA_ |
| not modelled | 48.4 | 16 | PDB header:transferase Chain: A: PDB Molecule:maltodextrin glycosyltransferase; PDBTitle: maltosyltransferase from thermotoga maritima
63 | c2qpuB_ |
| not modelled | 47.9 | 17 | PDB header:hydrolase Chain: B: PDB Molecule:alpha-amylase type a isozyme; PDBTitle: sugar tongs mutant s378p in complex with acarbose
64 | d1ea9c3 |
| not modelled | 47.8 | 17 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
65 | c1jibA_ |
| not modelled | 46.8 | 16 | PDB header:hydrolase Chain: A: PDB Molecule:neopullulanase; PDBTitle: complex of alpha-amylase ii (tva ii) from thermoactinomyces2 vulgaris r-47 with maltotetraose based on a crystal soaked3 with maltohexaose.
66 | c2z1kA_ |
| not modelled | 46.4 | 19 | PDB header:hydrolase Chain: A: PDB Molecule:(neo)pullulanase; PDBTitle: crystal structure of ttha1563 from thermus thermophilus hb8
67 | d1yhta1 |
| not modelled | 45.8 | 20 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:beta-N-acetylhexosaminidase catalytic domain
68 | c2zq0B_ |
| not modelled | 45.7 | 17 | PDB header:hydrolase Chain: B: PDB Molecule:alpha-glucosidase (alpha-glucosidase susb); PDBTitle: crystal structure of susb complexed with acarbose
69 | d2gjpa2 |
| not modelled | 44.5 | 13 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
70 | c2jvfA_ |
| not modelled | 44.1 | 12 | PDB header:de novo protein Chain: A: PDB Molecule:de novo protein m7; PDBTitle: solution structure of m7, a computationally-designed2 artificial protein
71 | c3czkA_ |
| not modelled | 43.4 | 16 | PDB header:hydrolase Chain: A: PDB Molecule:sucrose hydrolase; PDBTitle: crystal structure analysis of sucrose hydrolase(suh) e322q-2 sucrose complex
72 | d1u7pa_ |
| not modelled | 42.9 | 8 | Fold:HAD-like Superfamily:HAD-like Family:Magnesium-dependent phosphatase-1, Mdp1
73 | c1zjaB_ |
| not modelled | 42.8 | 14 | PDB header:isomerase Chain: B: PDB Molecule:trehalulose synthase; PDBTitle: crystal structure of the trehalulose synthase mutb from2 pseudomonas mesoacidophila mx-45 (triclinic form)
74 | c1qysA_ |
| not modelled | 42.3 | 9 | PDB header:de novo protein Chain: A: PDB Molecule:top7; PDBTitle: crystal structure of top7: a computationally designed2 protein with a novel fold
75 | d1ua7a2 |
| not modelled | 42.1 | 9 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
76 | c3dhuC_ |
| not modelled | 41.9 | 16 | PDB header:hydrolase Chain: C: PDB Molecule:alpha-amylase; PDBTitle: crystal structure of an alpha-amylase from lactobacillus2 plantarum
77 | c1ehaA_ |
| not modelled | 41.5 | 10 | PDB header:hydrolase Chain: A: PDB Molecule:glycosyltrehalose trehalohydrolase; PDBTitle: crystal structure of glycosyltrehalose trehalohydrolase2 from sulfolobus solfataricus
78 | c1gviA_ |
| not modelled | 40.9 | 15 | PDB header:hydrolase Chain: A: PDB Molecule:maltogenic amylase; PDBTitle: thermus maltogenic amylase in complex with beta-cd
79 | d1j0ha3 |
| not modelled | 40.8 | 15 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
80 | c2taaA_ |
| not modelled | 39.2 | 11 | PDB header:hydrolase (o-glycosyl) Chain: A: PDB Molecule:taka-amylase a; PDBTitle: structure and possible catalytic residues of taka-amylase a
81 | d1cyga4 |
| not modelled | 39.2 | 8 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
82 | c2dh3A_ |
| not modelled | 38.1 | 11 | PDB header:transport protein, signaling protein Chain: A: PDB Molecule:4f2 cell-surface antigen heavy chain; PDBTitle: crystal structure of human ed-4f2hc
83 | c3k8kB_ |
| not modelled | 38.1 | 19 | PDB header:membrane protein Chain: B: PDB Molecule:alpha-amylase, susg; PDBTitle: crystal structure of susg
84 | d1ud2a2 |
| not modelled | 37.4 | 16 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
85 | c1bagA_ |
| not modelled | 36.7 | 17 | PDB header:alpha-amylase Chain: A: PDB Molecule:alpha-1,4-glucan-4-glucanohydrolase; PDBTitle: alpha-amylase from bacillus subtilis complexed with2 maltopentaose
86 | c1jgiA_ |
| not modelled | 36.0 | 12 | PDB header:transferase Chain: A: PDB Molecule:amylosucrase; PDBTitle: crystal structure of the active site mutant glu328gln of2 amylosucrase from neisseria polysaccharea in complex with3 the natural substrate sucrose
87 | c1cygA_ |
| not modelled | 35.9 | 10 | PDB header:glycosyltransferase Chain: A: PDB Molecule:cyclodextrin glucanotransferase; PDBTitle: cyclodextrin glucanotransferase (e.c.2.4.1.19) (cgtase)
88 | c3gh7A_ |
| not modelled | 35.7 | 25 | PDB header:hydrolase Chain: A: PDB Molecule:beta-hexosaminidase; PDBTitle: crystal structure of beta-hexosaminidase from paenibacillus2 sp. ts12 in complex with galnac
89 | d1jaka1 |
| not modelled | 34.8 | 30 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:beta-N-acetylhexosaminidase catalytic domain
90 | d1mzha_ |
| not modelled | 34.6 | 11 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase
91 | d1z6ma1 |
| not modelled | 33.8 | 18 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:DsbA-like
92 | c2yl8A_ |
| not modelled | 33.7 | 18 | PDB header:hydrolase Chain: A: PDB Molecule:beta-n-acetylhexosaminidase; PDBTitle: inhibition of the pneumococcal virulence factor strh and2 molecular insights into n-glycan recognition and3 hydrolysis
93 | d1ht6a2 |
| not modelled | 33.7 | 17 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
94 | c3os4A_ |
| not modelled | 32.8 | 12 | PDB header:transferase Chain: A: PDB Molecule:nicotinate phosphoribosyltransferase; PDBTitle: the crystal structure of nicotinate phosphoribosyltransferase from2 yersinia pestis
95 | c3na8A_ |
| not modelled | 32.1 | 17 | PDB header:lyase Chain: A: PDB Molecule:putative dihydrodipicolinate synthetase; PDBTitle: crystal structure of a putative dihydrodipicolinate synthetase from2 pseudomonas aeruginosa
96 | c2rfgB_ |
| not modelled | 31.8 | 18 | PDB header:lyase Chain: B: PDB Molecule:dihydrodipicolinate synthase; PDBTitle: crystal structure of dihydrodipicolinate synthase from hahella2 chejuensis at 1.5a resolution
97 | d1pkla2 |
| not modelled | 31.7 | 9 | Fold:TIM beta/alpha-barrel Superfamily:Phosphoenolpyruvate/pyruvate domain Family:Pyruvate kinase
98 | c3bmwA_ |
| not modelled | 31.5 | 13 | PDB header:transferase Chain: A: PDB Molecule:cyclomaltodextrin glucanotransferase; PDBTitle: cyclodextrin glycosyl transferase from thermoanerobacterium2 thermosulfurigenes em1 mutant s77p complexed with a maltoheptaose3 inhibitor
99 | c3zt5D_ |
| not modelled | 31.4 | 18 | PDB header:hydrolase Chain: D: PDB Molecule:putative glucanohydrolase pep1a; PDBTitle: glge isoform 1 from streptomyces coelicolor with maltose2 bound
100 | d1yx1a1 |
| not modelled | 30.2 | 17 | Fold:TIM beta/alpha-barrel Superfamily:Xylose isomerase-like Family:KguE-like
101 | c3ngjC_ |
| not modelled | 30.0 | 10 | PDB header:lyase Chain: C: PDB Molecule:deoxyribose-phosphate aldolase; PDBTitle: crystal structure of a putative deoxyribose-phosphate aldolase from2 entamoeba histolytica
102 | c2ya1A_ |
| not modelled | 29.7 | 14 | PDB header:hydrolase Chain: A: PDB Molecule:putative alkaline amylopullulanase; PDBTitle: product complex of a multi-modular glycogen-degrading2 pneumococcal virulence factor spua
103 | d1o0ya_ |
| not modelled | 29.5 | 9 | Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I aldolase
104 | d1mxga2 |
| not modelled | 28.5 | 15 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
105 | d1avaa2 |
| not modelled | 27.7 | 17 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
106 | c1bplA_ |
| not modelled | 27.3 | 13 | PDB header:glycosyltransferase Chain: A: PDB Molecule:alpha-1,4-glucan-4-glucanohydrolase; PDBTitle: glycosyltransferase
107 | d1wzla3 |
| not modelled | 27.3 | 16 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
108 | c3faxA_ |
| not modelled | 27.0 | 14 | PDB header:hydrolase Chain: A: PDB Molecule:reticulocyte binding protein; PDBTitle: the crystal structure of gbs pullulanase sap in complex with2 maltotetraose
109 | d1yira1 |
| not modelled | 26.7 | 14 | Fold:TIM beta/alpha-barrel Superfamily:Nicotinate/Quinolinate PRTase C-terminal domain-like Family:Monomeric nicotinate phosphoribosyltransferase C-terminal domain
110 | c2kl5A_ |
| not modelled | 25.9 | 55 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein yutd; PDBTitle: solution nmr structure of protein yutd from b.subtilis, northeast2 structural genomics consortium target sr232
111 | d1d3ga_ |
| not modelled | 25.5 | 24 | Fold:TIM beta/alpha-barrel Superfamily:FMN-linked oxidoreductases Family:FMN-linked oxidoreductases
112 | d1nowa1 |
| not modelled | 25.0 | 18 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:beta-N-acetylhexosaminidase catalytic domain
113 | d1mioa_ |
| not modelled | 24.8 | 8 | Fold:Chelatase-like Superfamily:"Helical backbone" metal receptor Family:Nitrogenase iron-molybdenum protein
114 | c3n2xB_ |
| not modelled | 24.7 | 19 | PDB header:lyase Chain: B: PDB Molecule:uncharacterized protein yage; PDBTitle: crystal structure of yage, a prophage protein belonging to the2 dihydrodipicolinic acid synthase family from e. coli k12 in complex3 with pyruvate
115 | c2epoB_ |
| not modelled | 24.6 | 11 | PDB header:hydrolase Chain: B: PDB Molecule:n-acetyl-beta-d-glucosaminidase; PDBTitle: n-acetyl-b-d-glucosaminidase (gcna) from streptococcus gordonii
116 | c1e40A_ |
| not modelled | 24.3 | 11 | PDB header:hydrolase Chain: A: PDB Molecule:alpha-amylase; PDBTitle: tris/maltotriose complex of chimaeric amylase from b.2 amyloliquefaciens and b. licheniformis at 2.2a
117 | d1pbya1 |
| not modelled | 23.6 | 13 | Fold:Cytochrome c Superfamily:Cytochrome c Family:Quinohemoprotein amine dehydrogenase A chain, domains 1 and 2
118 | d2bhua3 |
| not modelled | 23.5 | 10 | Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:Amylase, catalytic domain
119 | c1tcmB_ |
| not modelled | 23.4 | 10 | PDB header:glycosyltransferase Chain: B: PDB Molecule:cyclodextrin glycosyltransferase; PDBTitle: cyclodextrin glycosyltransferase w616a mutant from bacillus2 circulans strain 251
120 | c1ud8A_ |
| not modelled | 22.8 | 13 | PDB header:hydrolase Chain: A: PDB Molecule:amylase; PDBTitle: crystal structure of amyk38 with lithium ion

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