Phyre 2 Results for P41039

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Email | l.a.kelley@imperial.ac.uk
Description | P41039
Date | Thu Jan 5 12:01:20 GMT 2012
Unique Job ID | 4ed97a43b2181352

Summary |

Top model
Image coloured by rainbow N → C terminus
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Model (left) based on template c2kgoA_
Top template information
PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein ybii; PDBTitle: solution nmr structure of zn finger protein ybil from escherichia2 coli. nesg target et107, ocsp target ec0402
Confidence and coverage
Confidence: | 100.0% | Coverage: | 100%
88 residues (100% 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 | G | W | A | N | D | D | A | V | N | E | Q | I | N | S | T | I | E | D | A | I | A | R | A | R | G | E | I | P | R | G | E | S | L | D | E | C | E | E | C | G | A | P | I | P | Q | A | R | R | E | A | I | P | G | V | R | L | C
Secondary structure |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
SS confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder |  | ? | ? | ? | ? | ? | ? | ? | ? | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  | ? | ? | ? |  | ? |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
Disorder confidence |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |  |
|  | . | . | . | . | . | . | . | . | . | 70 | . | . | . | . | . | . | . | . | . | 80 | . | . | . | . | . | . | . | .
Sequence |  | I | H | C | Q | Q | E | K | D | L | Q | K | P | A | Y | T | G | Y | N | R | R | G | S | K | D | S | Q | L | R
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 |
| c2kgoA_ |

### PDB 2kgo chain A

Region: 1 - 88
Aligned: 88
Modelled: 88
Confidence: 100.0%
Identity: 100%
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein ybii;
PDBTitle: solution nmr structure of zn finger protein ybil from escherichia2 coli. nesg target et107, ocsp target ec0402

Phyre2
2 |
| c1tjlD_ |

### PDB 1tjl chain D

Region: 9 - 76
Aligned: 67
Modelled: 68
Confidence: 99.9%
Identity: 25%
PDB header:transcription
Chain: D: PDB Molecule:dnak suppressor protein;
PDBTitle: crystal structure of transcription factor dksa from e. coli

Phyre2
3 |
| c2kq9A_ |

### PDB 2kq9 chain A

Region: 16 - 66
Aligned: 50
Modelled: 51
Confidence: 99.7%
Identity: 28%
PDB header:transcription
Chain: A: PDB Molecule:dnak suppressor protein;
PDBTitle: solution structure of dnak suppressor protein from2 agrobacterium tumefaciens c58. northeast structural3 genomics consortium target att12/ontario center for4 structural proteomics target atc0888

Phyre2
4 |
| d1tjla2 |

### PDB 1tjl chain A domain 2

Region: 36 - 76
Aligned: 41
Modelled: 41
Confidence: 99.5%
Identity: 34%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: Prokaryotic DksA/TraR C4-type zinc finger

Phyre2
5 |
| c2gviA_ |

### PDB 2gvi chain A

Region: 38 - 65
Aligned: 28
Modelled: 28
Confidence: 77.1%
Identity: 21%
PDB header:oxidoreductase
Chain: A: PDB Molecule:conserved hypothetical protein;
PDBTitle: crystal structure of a putative formylmethanofuran dehydrogenase2 subunit e (ta1109) from thermoplasma acidophilum at 1.87 a resolution

Phyre2
6 |
| c2p57A_ |

### PDB 2p57 chain A

Region: 21 - 75
Aligned: 54
Modelled: 55
Confidence: 69.7%
Identity: 22%
PDB header:metal binding protein
Chain: A: PDB Molecule:gtpase-activating protein znf289;
PDBTitle: gap domain of znf289, an id1-regulated zinc finger protein

Phyre2
7 |
| c3d00A_ |

### PDB 3d00 chain A

Region: 38 - 65
Aligned: 22
Modelled: 28
Confidence: 59.0%
Identity: 41%
PDB header:metal binding protein
Chain: A: PDB Molecule:tungsten formylmethanofuran dehydrogenase subunit e;
PDBTitle: crystal structure of a tungsten formylmethanofuran dehydrogenase2 subunit e (fmde)-like protein (syn_00638) from syntrophus3 aciditrophicus at 1.90 a resolution

Phyre2
8 |
| d1dcqa2 |

### PDB 1dcq chain A domain 2

Region: 24 - 67
Aligned: 43
Modelled: 44
Confidence: 58.3%
Identity: 30%
Fold: ArfGap/RecO-like zinc finger
Superfamily: ArfGap/RecO-like zinc finger
Family: Pyk2-associated protein beta ARF-GAP domain

Phyre2
9 |
| c2d9lA_ |

### PDB 2d9l chain A

Region: 24 - 67
Aligned: 43
Modelled: 44
Confidence: 55.9%
Identity: 14%
PDB header:gene regulation
Chain: A: PDB Molecule:nucleoporin-like protein rip;
PDBTitle: solution structure of the arfgap domain of human rip

Phyre2
10 |
| c3mhsE_ |

### PDB 3mhs chain E

Region: 36 - 46
Aligned: 11
Modelled: 11
Confidence: 55.8%
Identity: 45%
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

Phyre2
11 |
| c2b0oF_ |

### PDB 2b0o chain F

Region: 24 - 78
Aligned: 54
Modelled: 55
Confidence: 52.3%
Identity: 20%
PDB header:metal binding protein
Chain: F: PDB Molecule:uplc1;
PDBTitle: crystal structure of uplc1 gap domain

Phyre2
12 |
| c3fehA_ |

### PDB 3feh chain A

Region: 17 - 67
Aligned: 50
Modelled: 51
Confidence: 50.5%
Identity: 26%
PDB header:hydrolase activator
Chain: A: PDB Molecule:centaurin-alpha-1;
PDBTitle: crystal structure of full length centaurin alpha-1

Phyre2
13 |
| d1wyha1 |

### PDB 1wyh chain A domain 1

Region: 38 - 67
Aligned: 30
Modelled: 30
Confidence: 48.6%
Identity: 23%
Fold: Glucocorticoid receptor-like (DNA-binding domain)
Superfamily: Glucocorticoid receptor-like (DNA-binding domain)
Family: LIM domain

Phyre2
14 |
| c1dcqA_ |

### PDB 1dcq chain A

Region: 24 - 78
Aligned: 54
Modelled: 55
Confidence: 48.5%
Identity: 26%
PDB header:metal binding protein
Chain: A: PDB Molecule:pyk2-associated protein beta;
PDBTitle: crystal structure of the arf-gap domain and ankyrin repeats2 of papbeta.

Phyre2
15 |
| c2iqjB_ |

### PDB 2iqj chain B

Region: 24 - 67
Aligned: 36
Modelled: 44
Confidence: 48.0%
Identity: 28%
PDB header:protein transport
Chain: B: PDB Molecule:stromal membrane-associated protein 1-like;
PDBTitle: crystal structure of the gap domain of smap1l (loc64744)2 stromal membrane-associated protein 1-like

Phyre2
16 |
| c2owaB_ |

### PDB 2owa chain B

Region: 24 - 75
Aligned: 51
Modelled: 52
Confidence: 47.7%
Identity: 12%
PDB header:protein transport
Chain: B: PDB Molecule:arfgap-like finger domain containing protein;
PDBTitle: crystal structure of putative gtpase activating protein for2 adp ribosylation factor from cryptosporidium parvum3 (cgd5_1040)

Phyre2
17 |
| c3lvrE_ |

### PDB 3lvr chain E

Region: 24 - 78
Aligned: 54
Modelled: 55
Confidence: 47.6%
Identity: 20%
PDB header:protein transport
Chain: E: PDB Molecule:arf-gap with sh3 domain, ank repeat and ph domain-
PDBTitle: the crystal structure of asap3 in complex with arf6 in transition2 state soaked with calcium

Phyre2
18 |
| c3dwdB_ |

### PDB 3dwd chain B

Region: 24 - 67
Aligned: 43
Modelled: 44
Confidence: 47.2%
Identity: 26%
PDB header:transport protein
Chain: B: PDB Molecule:adp-ribosylation factor gtpase-activating protein 1;
PDBTitle: crystal structure of the arfgap domain of human arfgap1

Phyre2
19 |
| c3jueA_ |

### PDB 3jue chain A

Region: 26 - 78
Aligned: 52
Modelled: 53
Confidence: 45.6%
Identity: 19%
PDB header:protein transport/endocytosis
Chain: A: PDB Molecule:arfgap with coiled-coil, ank repeat and ph domain-
PDBTitle: crystal structure of arfgap and ank repeat domain of acap1

Phyre2
20 |
| d1x4ka1 |

### PDB 1x4k chain A domain 1

Region: 38 - 67
Aligned: 30
Modelled: 30
Confidence: 44.7%
Identity: 20%
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 | c2kgoA_ |
|  | 100.0 | 100 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein ybii; PDBTitle: solution nmr structure of zn finger protein ybil from escherichia2 coli. nesg target et107, ocsp target ec0402
2 | c1tjlD_ |
|  | 99.9 | 25 | PDB header:transcription Chain: D: PDB Molecule:dnak suppressor protein; PDBTitle: crystal structure of transcription factor dksa from e. coli
3 | c2kq9A_ |
|  | 99.7 | 28 | PDB header:transcription Chain: A: PDB Molecule:dnak suppressor protein; PDBTitle: solution structure of dnak suppressor protein from2 agrobacterium tumefaciens c58. northeast structural3 genomics consortium target att12/ontario center for4 structural proteomics target atc0888
4 | d1tjla2 |
|  | 99.5 | 34 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:Prokaryotic DksA/TraR C4-type zinc finger
5 | c2gviA_ |
|  | 77.1 | 21 | PDB header:oxidoreductase Chain: A: PDB Molecule:conserved hypothetical protein; PDBTitle: crystal structure of a putative formylmethanofuran dehydrogenase2 subunit e (ta1109) from thermoplasma acidophilum at 1.87 a resolution
6 | c2p57A_ |
|  | 69.7 | 22 | PDB header:metal binding protein Chain: A: PDB Molecule:gtpase-activating protein znf289; PDBTitle: gap domain of znf289, an id1-regulated zinc finger protein
7 | c3d00A_ |
|  | 59.0 | 41 | PDB header:metal binding protein Chain: A: PDB Molecule:tungsten formylmethanofuran dehydrogenase subunit e; PDBTitle: crystal structure of a tungsten formylmethanofuran dehydrogenase2 subunit e (fmde)-like protein (syn_00638) from syntrophus3 aciditrophicus at 1.90 a resolution
8 | d1dcqa2 |
|  | 58.3 | 30 | Fold:ArfGap/RecO-like zinc finger Superfamily:ArfGap/RecO-like zinc finger Family:Pyk2-associated protein beta ARF-GAP domain
9 | c2d9lA_ |
|  | 55.9 | 14 | PDB header:gene regulation Chain: A: PDB Molecule:nucleoporin-like protein rip; PDBTitle: solution structure of the arfgap domain of human rip
10 | c3mhsE_ |
|  | 55.8 | 45 | 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
11 | c2b0oF_ |
|  | 52.3 | 20 | PDB header:metal binding protein Chain: F: PDB Molecule:uplc1; PDBTitle: crystal structure of uplc1 gap domain
12 | c3fehA_ |
|  | 50.5 | 26 | PDB header:hydrolase activator Chain: A: PDB Molecule:centaurin-alpha-1; PDBTitle: crystal structure of full length centaurin alpha-1
13 | d1wyha1 |
|  | 48.6 | 23 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
14 | c1dcqA_ |
|  | 48.5 | 26 | PDB header:metal binding protein Chain: A: PDB Molecule:pyk2-associated protein beta; PDBTitle: crystal structure of the arf-gap domain and ankyrin repeats2 of papbeta.
15 | c2iqjB_ |
|  | 48.0 | 28 | PDB header:protein transport Chain: B: PDB Molecule:stromal membrane-associated protein 1-like; PDBTitle: crystal structure of the gap domain of smap1l (loc64744)2 stromal membrane-associated protein 1-like
16 | c2owaB_ |
|  | 47.7 | 12 | PDB header:protein transport Chain: B: PDB Molecule:arfgap-like finger domain containing protein; PDBTitle: crystal structure of putative gtpase activating protein for2 adp ribosylation factor from cryptosporidium parvum3 (cgd5_1040)
17 | c3lvrE_ |
|  | 47.6 | 20 | PDB header:protein transport Chain: E: PDB Molecule:arf-gap with sh3 domain, ank repeat and ph domain- PDBTitle: the crystal structure of asap3 in complex with arf6 in transition2 state soaked with calcium
18 | c3dwdB_ |
|  | 47.2 | 26 | PDB header:transport protein Chain: B: PDB Molecule:adp-ribosylation factor gtpase-activating protein 1; PDBTitle: crystal structure of the arfgap domain of human arfgap1
19 | c3jueA_ |
|  | 45.6 | 19 | PDB header:protein transport/endocytosis Chain: A: PDB Molecule:arfgap with coiled-coil, ank repeat and ph domain- PDBTitle: crystal structure of arfgap and ank repeat domain of acap1
20 | d1x4ka1 |
|  | 44.7 | 20 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
21 | c3o47A_ |
| not modelled | 40.3 | 19 | PDB header:hydrolase, hydrolase activator Chain: A: PDB Molecule:adp-ribosylation factor gtpase-activating protein 1, adp- PDBTitle: crystal structure of arfgap1-arf1 fusion protein
22 | d1tjla1 |
| not modelled | 39.7 | 5 | Fold:Long alpha-hairpin Superfamily:DnaK suppressor protein DksA, alpha-hairpin domain Family:DnaK suppressor protein DksA, alpha-hairpin domain
23 | d2cura1 |
| not modelled | 39.5 | 23 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
24 | d1rutx1 |
| not modelled | 36.4 | 42 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
25 | d1j2oa1 |
| not modelled | 34.4 | 46 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
26 | d1rutx3 |
| not modelled | 26.4 | 36 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
27 | d2dloa1 |
| not modelled | 21.5 | 30 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
28 | c2d8zA_ |
| not modelled | 20.3 | 20 | PDB header:signaling protein, structural protein Chain: A: PDB Molecule:four and a half lim domains 2; PDBTitle: solution structure of the third lim domain of four and a2 half lim domains protein 2 (fhl-2)
29 | d1x3ha1 |
| not modelled | 17.6 | 24 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
30 | c2curA_ |
| not modelled | 17.0 | 23 | PDB header:metal binding protein Chain: A: PDB Molecule:skeletal muscle lim-protein 1; PDBTitle: solution structure of skeletal muscle lim-protein 1
31 | c2d8xA_ |
| not modelled | 15.3 | 20 | PDB header:structural protein, cell cycle Chain: A: PDB Molecule:protein pinch; PDBTitle: solution structure of the second lim domain of particularly2 interesting new cys-his protein (pinch)
32 | c2darA_ |
| not modelled | 15.0 | 17 | PDB header:metal binding protein Chain: A: PDB Molecule:pdz and lim domain protein 5; PDBTitle: solution structure of first lim domain of enigma-like pdz2 and lim domains protein
33 | d1xpaa2 |
| not modelled | 14.5 | 50 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:DNA repair factor XPA DNA- and RPA-binding domain, N-terminal subdomain
34 | c2gb5B_ |
| not modelled | 14.3 | 23 | PDB header:hydrolase Chain: B: PDB Molecule:nadh pyrophosphatase; PDBTitle: crystal structure of nadh pyrophosphatase (ec 3.6.1.22) (1790429) from2 escherichia coli k12 at 2.30 a resolution
35 | c1j2oA_ |
| not modelled | 14.2 | 46 | PDB header:metal binding protein Chain: A: PDB Molecule:fusion of rhombotin-2 and lim domain-binding PDBTitle: structure of flin2, a complex containing the n-terminal lim2 domain of lmo2 and ldb1-lid
36 | c1nnjA_ |
| not modelled | 14.1 | 25 | PDB header:hydrolase Chain: A: PDB Molecule:formamidopyrimidine-dna glycosylase; PDBTitle: crystal structure complex between the lactococcus lactis fpg and an2 abasic site containing dna
37 | d2cuqa1 |
| not modelled | 13.7 | 19 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
38 | d1x63a2 |
| not modelled | 13.3 | 19 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
39 | c1x4lA_ |
| not modelled | 12.5 | 18 | PDB header:metal binding protein Chain: A: PDB Molecule:skeletal muscle lim-protein 3; PDBTitle: solution structure of lim domain in four and a half lim2 domains protein 2
40 | c1wyhA_ |
| not modelled | 12.2 | 23 | PDB header:metal binding protein Chain: A: PDB Molecule:skeletal muscle lim-protein 2; PDBTitle: solution structure of the lim domain from human skeletal2 muscle lim-protein 2
41 | c1wjvA_ |
| not modelled | 11.5 | 28 | PDB header:dna binding protein Chain: A: PDB Molecule:cell growth regulating nucleolar protein lyar; PDBTitle: solution structure of the n-terminal zinc finger domain of2 mouse cell growth regulating nucleolar protein lyar
42 | c2cuqA_ |
| not modelled | 11.5 | 20 | PDB header:structural genomics, unknown function Chain: A: PDB Molecule:four and a half lim domains 3; PDBTitle: solution structure of second lim domain from human skeletal2 muscle lim-protein 2
43 | d1ee8a3 |
| not modelled | 11.3 | 28 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins
44 | c3f6qB_ |
| not modelled | 11.2 | 24 | PDB header:signaling protein/signaling protein Chain: B: PDB Molecule:lim and senescent cell antigen-like-containing PDBTitle: crystal structure of integrin-linked kinase ankyrin repeat2 domain in complex with pinch1 lim1 domain
45 | c1x64A_ |
| not modelled | 11.2 | 17 | PDB header:contractile protein Chain: A: PDB Molecule:alpha-actinin-2 associated lim protein; PDBTitle: solution structure of the lim domain of alpha-actinin-22 associated lim protein
46 | d2cupa3 |
| not modelled | 11.1 | 56 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
47 | d1jmxa5 |
| not modelled | 11.1 | 45 | Fold:Streptavidin-like Superfamily:Quinohemoprotein amine dehydrogenase A chain, domain 3 Family:Quinohemoprotein amine dehydrogenase A chain, domain 3
48 | d2dara2 |
| not modelled | 10.6 | 33 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
49 | c1x63A_ |
| not modelled | 10.3 | 21 | PDB header:contractile protein Chain: A: PDB Molecule:skeletal muscle lim-protein 1; PDBTitle: solution structure of the second lim domain of skeletal2 muscle lim protein 1
50 | d1m3va1 |
| not modelled | 10.2 | 36 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
51 | c1d4uA_ |
| not modelled | 9.8 | 25 | PDB header:dna binding protein Chain: A: PDB Molecule:nucleotide excision repair protein xpa (xpa-mbd); PDBTitle: interactions of human nucleotide excision repair protein2 xpa with rpa70 and dna: chemical shift mapping and 15n nmr3 relaxation studies
52 | c2egqA_ |
| not modelled | 9.3 | 18 | PDB header:structural protein Chain: A: PDB Molecule:fhl1 protein; PDBTitle: solution structure of the fourth lim domain from human four2 and a half lim domains 1
53 | d1x4la2 |
| not modelled | 9.2 | 44 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
54 | c3na7A_ |
| not modelled | 9.2 | 15 | PDB header:gene regulation, chaperone Chain: A: PDB Molecule:hp0958; PDBTitle: 2.2 angstrom structure of the hp0958 protein from helicobacter pylori2 ccug 17874
55 | d2d8za2 |
| not modelled | 9.0 | 23 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
56 | d2cora1 |
| not modelled | 9.0 | 29 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
57 | c2o10A_ |
| not modelled | 8.3 | 20 | PDB header:metal binding protein Chain: A: PDB Molecule:muscle lim protein; PDBTitle: solution structure of the n-terminal lim domain of mlp/crp3
58 | c2hyxA_ |
| not modelled | 8.3 | 27 | PDB header:unknown function Chain: A: PDB Molecule:protein dipz; PDBTitle: structure of the c-terminal domain of dipz from mycobacterium2 tuberculosis
59 | c1x4kA_ |
| not modelled | 7.8 | 21 | PDB header:metal binding protein Chain: A: PDB Molecule:skeletal muscle lim-protein 3; PDBTitle: solution structure of lim domain in lim-protein 3
60 | c1x61A_ |
| not modelled | 7.6 | 21 | PDB header:cell adhesion Chain: A: PDB Molecule:thyroid receptor interacting protein 6; PDBTitle: solution structure of the first lim domain of thyroid2 receptor interacting protein 6 (trip6)
61 | c1x3hA_ |
| not modelled | 7.3 | 14 | PDB header:metal binding protein Chain: A: PDB Molecule:leupaxin; PDBTitle: solution structure of the lim domain of human leupaxin
62 | d1twfj_ |
| not modelled | 7.2 | 33 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:RNA polymerase subunit RPB10 Family:RNA polymerase subunit RPB10
63 | c2l4zA_ |
| not modelled | 7.0 | 43 | PDB header:hydrolase, metal binding protein Chain: A: PDB Molecule:dna endonuclease rbbp8, lim domain transcription factor PDBTitle: nmr structure of fusion of ctip (641-685) to lmo4-lim1 (18-82)
64 | c2ko5A_ |
| not modelled | 6.8 | 40 | PDB header:transcription Chain: A: PDB Molecule:ring finger protein z; PDBTitle: nmr solution structure of lfv-z
65 | d1pbya5 |
| not modelled | 6.8 | 8 | Fold:Streptavidin-like Superfamily:Quinohemoprotein amine dehydrogenase A chain, domain 3 Family:Quinohemoprotein amine dehydrogenase A chain, domain 3
66 | c2d8yA_ |
| not modelled | 6.8 | 16 | PDB header:structural protein Chain: A: PDB Molecule:eplin protein; PDBTitle: solution structure of the lim domain of epithelial protein2 lost in neoplasm
67 | c1ibiA_ |
| not modelled | 6.6 | 23 | PDB header:metal binding protein Chain: A: PDB Molecule:cysteine-rich protein 2; PDBTitle: quail cysteine and glycine-rich protein, nmr, 15 minimized2 model structures
68 | d1u5sb1 |
| not modelled | 6.4 | 44 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
69 | c1jmxA_ |
| not modelled | 6.2 | 42 | PDB header:oxidoreductase Chain: A: PDB Molecule:amine dehydrogenase; PDBTitle: crystal structure of a quinohemoprotein amine dehydrogenase2 from pseudomonas putida
70 | d1v6ga1 |
| not modelled | 6.2 | 33 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
71 | c2i5oA_ |
| not modelled | 6.0 | 56 | PDB header:transferase Chain: A: PDB Molecule:dna polymerase eta; PDBTitle: solution structure of the ubiquitin-binding zinc finger2 (ubz) domain of the human dna y-polymerase eta
72 | c2qgpA_ |
| not modelled | 6.0 | 24 | PDB header:hydrolase Chain: A: PDB Molecule:hnh endonuclease; PDBTitle: x-ray structure of the nhn endonuclease from geobacter2 metallireducens. northeast structural genomics consortium3 target gmr87.
73 | d1ef4a_ |
| not modelled | 5.9 | 50 | Fold:DNA/RNA-binding 3-helical bundle Superfamily:RNA polymerase subunit RPB10 Family:RNA polymerase subunit RPB10
74 | d1i5ga_ |
| not modelled | 5.9 | 7 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like
75 | c2a20A_ |
| not modelled | 5.8 | 18 | PDB header:metal binding protein Chain: A: PDB Molecule:regulating synaptic membrane exocytosis protein PDBTitle: solution structure of rim2 zinc finger domain
76 | c1rutX_ |
| not modelled | 5.8 | 42 | PDB header:protein binding Chain: X: PDB Molecule:fusion protein of lmo4 protein and lim domain- PDBTitle: complex of lmo4 lim domains 1 and 2 with the ldb1 lid domain
77 | c2f9iD_ |
| not modelled | 5.8 | 17 | PDB header:transferase Chain: D: PDB Molecule:acetyl-coenzyme a carboxylase carboxyl PDBTitle: crystal structure of the carboxyltransferase subunit of acc2 from staphylococcus aureus
78 | c1a7iA_ |
| not modelled | 5.7 | 17 | PDB header:lim domain containing proteins Chain: A: PDB Molecule:qcrp2 (lim1); PDBTitle: amino-terminal lim domain from quail cysteine and glycine-2 rich protein, nmr, minimized average structure
79 | d1o73a_ |
| not modelled | 5.6 | 11 | Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Glutathione peroxidase-like
80 | c3a44D_ |
| not modelled | 5.6 | 22 | PDB header:metal binding protein Chain: D: PDB Molecule:hydrogenase nickel incorporation protein hypa; PDBTitle: crystal structure of hypa in the dimeric form
81 | c1u5kA_ |
| not modelled | 5.6 | 33 | PDB header:recombination,replication Chain: A: PDB Molecule:hypothetical protein; PDBTitle: recombinational repair protein reco
82 | d2ak3a2 |
| not modelled | 5.6 | 20 | Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain
83 | d1qo8a1 |
| not modelled | 5.5 | 13 | Fold:Multiheme cytochromes Superfamily:Multiheme cytochromes Family:Di-heme elbow motif
84 | c1nypA_ |
| not modelled | 5.5 | 20 | PDB header:cell adhesion Chain: A: PDB Molecule:pinch protein; PDBTitle: 4th lim domain of pinch protein
85 | c2dloA_ |
| not modelled | 5.4 | 42 | PDB header:cell adhesion Chain: A: PDB Molecule:thyroid receptor-interacting protein 6; PDBTitle: solution structure of the second lim domain of human2 thyroid receptor-interacting protein 6
86 | d1e4va2 |
| not modelled | 5.4 | 10 | Fold:Rubredoxin-like Superfamily:Microbial and mitochondrial ADK, insert "zinc finger" domain Family:Microbial and mitochondrial ADK, insert "zinc finger" domain
87 | c2pmzN_ |
| not modelled | 5.3 | 50 | PDB header:translation, transferase Chain: N: PDB Molecule:dna-directed rna polymerase subunit n; PDBTitle: archaeal rna polymerase from sulfolobus solfataricus
88 | c2o13A_ |
| not modelled | 5.3 | 21 | PDB header:metal binding protein Chain: A: PDB Molecule:muscle lim protein; PDBTitle: solution structure of the c-terminal lim domain of mlp/crp3
89 | c2cu8A_ |
| not modelled | 5.2 | 20 | PDB header:metal binding protein Chain: A: PDB Molecule:cysteine-rich protein 2; PDBTitle: solution structure of the lim domain of human cysteine-rich2 protein 2
90 | d1kcfa1 |
| not modelled | 5.1 | 57 | Fold:LEM/SAP HeH motif Superfamily:SAP domain Family:SAP domain
91 | d1ibia2 |
| not modelled | 5.1 | 21 | Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain
92 | c3hi2C_ |
| not modelled | 5.1 | 33 | PDB header:dna binding protein/toxin Chain: C: PDB Molecule:hth-type transcriptional regulator mqsa(ygit); PDBTitle: structure of the n-terminal domain of the e. coli antitoxin mqsa2 (ygit/b3021) in complex with the e. coli toxin mqsr (ygiu/b3022)

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