Phyre Home Retrieve Phyre Job Id
Emaill.a.kelley@imperial.ac.uk
DescriptionP41271
DateSat Jun 16 10:47:59 BST 2012
Unique Job IDe43169832b7ce691

Summary 

Top model
Image coloured by rainbow N → C terminus
Model (left) based on template d1hcnb_
Top template information
Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Gonadodropin/Follitropin
Confidence and coverage
Confidence: 98.7% Coverage: 52%
94 residues ( 52% of your sequence) have been modelled with 98.7% confidence by the single highest scoring template.
You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library.
3D viewing
Interactive 3D view in Jmol

Sequence analysis 

Secondary structure and disorder prediction 

   1........10.........20.........30.........40.........50.........60
Sequence  MLRVLVGAVLPAMLLAAPPPINKLALFPDKSAWCEAKNITQIVGHSGCEAKSIQNRACLG
Secondary structure 
SS confidence 
Disorder  ?????
??????
??
Disorder confidence 
 
   .........70.........80.........90.........100.........110.........120
Sequence  QCFSYSVPNTFPQSTESLVHCDSCMPAQSMWEIVTLECPGHEEVPRVDKLVEKILHCSCQ
Secondary structure 
SS confidence 
Disorder 
?
??????
????
?
Disorder confidence 
 
   .........130.........140.........150.........160.........170.........180
Sequence  ACGKEPSHEGLSVYVQGEDGPGSQPGTHPHPHPHPHPGGQTPEPEDPPGAPHTEEEGAED
Secondary structure 
SS confidence 
Disorder  ?????????
?????????????????????????????????????????????????
Disorder confidence 
 
  
Sequence 
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

RankAligned region

PDB 1hcn chain B

3D model

Region: 29 - 128
Aligned: 94
Modelled: 98
Confidence: 98.7%
Identity: 21%
Fold: Cystine-knot cytokines
Superfamily: Cystine-knot cytokines
Family: Gonadodropin/Follitropin

Phyre2

PDB 1qfw chain B

3D model

Region: 29 - 128
Aligned: 94
Modelled: 98
Confidence: 98.7%
Identity: 21%
PDB header:immune system
Chain: B: PDB Molecule:gonadotrophin beta subunit;
PDBTitle: ternary complex of human chorionic gonadotropin with fv anti alpha2 subunit and fv anti beta subunit

Phyre2

PDB 1xwd chain B domain 1

3D model

Region: 34 - 128
Aligned: 89
Modelled: 93
Confidence: 98.6%
Identity: 21%
Fold: Cystine-knot cytokines
Superfamily: Cystine-knot cytokines
Family: Gonadodropin/Follitropin

Phyre2

PDB 2k8p chain A

3D model

Region: 33 - 120
Aligned: 86
Modelled: 88
Confidence: 97.4%
Identity: 24%
PDB header:signaling protein
Chain: A: PDB Molecule:sclerostin;
PDBTitle: characterisation of the structural features and2 interactions of sclerostin: molecular insight into a key3 regulator of wnt-mediated bone formation

Phyre2

PDB 2kd3 chain A

3D model

Region: 33 - 120
Aligned: 79
Modelled: 81
Confidence: 96.9%
Identity: 23%
PDB header:protein binding
Chain: A: PDB Molecule:sclerostin;
PDBTitle: nmr structure of the wnt modulator protein sclerostin

Phyre2

PDB 3evs chain B

3D model

Region: 50 - 120
Aligned: 68
Modelled: 71
Confidence: 95.1%
Identity: 18%
PDB header:cytokine/transferase receptor
Chain: B: PDB Molecule:growth/differentiation factor 5;
PDBTitle: crystal structure of the gdf-5:bmp receptor ib complex.

Phyre2

PDB 2qcq chain A

3D model

Region: 50 - 120
Aligned: 68
Modelled: 71
Confidence: 95.0%
Identity: 19%
PDB header:signaling protein
Chain: A: PDB Molecule:bone morphogenetic protein 3;
PDBTitle: crystal structure of bone morphogenetic protein-3 (bmp-3)

Phyre2

PDB 2arp chain A domain 1

3D model

Region: 50 - 120
Aligned: 68
Modelled: 68
Confidence: 94.8%
Identity: 16%
Fold: Cystine-knot cytokines
Superfamily: Cystine-knot cytokines
Family: Transforming growth factor (TGF)-beta

Phyre2

PDB 2gyr chain B

3D model

Region: 33 - 119
Aligned: 82
Modelled: 87
Confidence: 94.6%
Identity: 16%
PDB header:hormone/growth factor
Chain: B: PDB Molecule:neurotrophic factor artemin, isoform 3;
PDBTitle: crystal structure of human artemin

Phyre2

PDB 2h62 chain A domain 1

3D model

Region: 50 - 120
Aligned: 67
Modelled: 71
Confidence: 94.6%
Identity: 18%
Fold: Cystine-knot cytokines
Superfamily: Cystine-knot cytokines
Family: Transforming growth factor (TGF)-beta

Phyre2

PDB 1lxi chain A

3D model

Region: 50 - 119
Aligned: 66
Modelled: 70
Confidence: 94.6%
Identity: 17%
Fold: Cystine-knot cytokines
Superfamily: Cystine-knot cytokines
Family: Transforming growth factor (TGF)-beta

Phyre2

PDB 1zkz chain A

3D model

Region: 50 - 120
Aligned: 70
Modelled: 71
Confidence: 93.9%
Identity: 17%
PDB header:hormone/growth factor
Chain: A: PDB Molecule:growth/differentiation factor 2;
PDBTitle: crystal structure of bmp9

Phyre2

PDB 3hh2 chain B

3D model

Region: 50 - 120
Aligned: 64
Modelled: 71
Confidence: 93.6%
Identity: 14%
PDB header:signaling protein/cytokine
Chain: B: PDB Molecule:growth/differentiation factor 8;
PDBTitle: crystal structure of the myostatin:follistatin 288 complex

Phyre2

PDB 2qcw chain B

3D model

Region: 50 - 119
Aligned: 67
Modelled: 70
Confidence: 93.6%
Identity: 18%
PDB header:signaling protein
Chain: B: PDB Molecule:bone morphogenetic protein 6;
PDBTitle: crystal structure of bone morphogenetic protein-6 (bmp-6)

Phyre2

PDB 1pdg chain A

3D model

Region: 27 - 121
Aligned: 80
Modelled: 88
Confidence: 92.6%
Identity: 19%
Fold: Cystine-knot cytokines
Superfamily: Cystine-knot cytokines
Family: Platelet-derived growth factor-like

Phyre2

PDB 1agq chain B

3D model

Region: 30 - 119
Aligned: 84
Modelled: 90
Confidence: 92.1%
Identity: 19%
PDB header:growth factor
Chain: B: PDB Molecule:glial cell-derived neurotrophic factor;
PDBTitle: glial cell-derived neurotrophic factor from rat

Phyre2

PDB 2xv7 chain A

3D model

Region: 30 - 121
Aligned: 77
Modelled: 85
Confidence: 92.1%
Identity: 19%
PDB header:hormone
Chain: A: PDB Molecule:vascular endothelial growth factor d;
PDBTitle: crystal structure of vascular endothelial growth factor d

Phyre2

PDB 3mjk chain E

3D model

Region: 23 - 120
Aligned: 79
Modelled: 98
Confidence: 91.4%
Identity: 23%
PDB header:hormone
Chain: E: PDB Molecule:platelet-derived growth factor subunit a;
PDBTitle: structure of a growth factor precursor

Phyre2

PDB 1ktz chain A

3D model

Region: 50 - 120
Aligned: 57
Modelled: 61
Confidence: 90.7%
Identity: 16%
Fold: Cystine-knot cytokines
Superfamily: Cystine-knot cytokines
Family: Transforming growth factor (TGF)-beta

Phyre2

PDB 1agq chain A

3D model

Region: 33 - 119
Aligned: 83
Modelled: 87
Confidence: 90.5%
Identity: 19%
Fold: Cystine-knot cytokines
Superfamily: Cystine-knot cytokines
Family: Transforming growth factor (TGF)-beta

Phyre2
1
d1hcnb_
2
c1qfwB_
3
d1xwdb1
4
c2k8pA_
5
c2kd3A_
6
c3evsB_
7
c2qcqA_
8
d2arpa1
9
c2gyrB_
10
d2h62a1
11
d1lxia_
12
c1zkzA_
13
c3hh2B_
14
c2qcwB_
15
d1pdga_
16
c1agqB_
17
c2xv7A_
18
c3mjkE_
19
d1ktza_
20
d1agqa_
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70



Detailed template information 

#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1d1hcnb_
98.7 21 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Gonadodropin/Follitropin
2c1qfwB_
98.7 21 PDB header:immune system
Chain: B: PDB Molecule:gonadotrophin beta subunit;
PDBTitle: ternary complex of human chorionic gonadotropin with fv anti alpha2 subunit and fv anti beta subunit
3d1xwdb1
98.6 21 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Gonadodropin/Follitropin
4c2k8pA_
97.4 24 PDB header:signaling protein
Chain: A: PDB Molecule:sclerostin;
PDBTitle: characterisation of the structural features and2 interactions of sclerostin: molecular insight into a key3 regulator of wnt-mediated bone formation
5c2kd3A_
96.9 23 PDB header:protein binding
Chain: A: PDB Molecule:sclerostin;
PDBTitle: nmr structure of the wnt modulator protein sclerostin
6c3evsB_
95.1 18 PDB header:cytokine/transferase receptor
Chain: B: PDB Molecule:growth/differentiation factor 5;
PDBTitle: crystal structure of the gdf-5:bmp receptor ib complex.
7c2qcqA_
95.0 19 PDB header:signaling protein
Chain: A: PDB Molecule:bone morphogenetic protein 3;
PDBTitle: crystal structure of bone morphogenetic protein-3 (bmp-3)
8d2arpa1
94.8 16 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Transforming growth factor (TGF)-beta
9c2gyrB_
94.6 16 PDB header:hormone/growth factor
Chain: B: PDB Molecule:neurotrophic factor artemin, isoform 3;
PDBTitle: crystal structure of human artemin
10d2h62a1
94.6 18 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Transforming growth factor (TGF)-beta
11d1lxia_
94.6 17 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Transforming growth factor (TGF)-beta
12c1zkzA_
93.9 17 PDB header:hormone/growth factor
Chain: A: PDB Molecule:growth/differentiation factor 2;
PDBTitle: crystal structure of bmp9
13c3hh2B_
93.6 14 PDB header:signaling protein/cytokine
Chain: B: PDB Molecule:growth/differentiation factor 8;
PDBTitle: crystal structure of the myostatin:follistatin 288 complex
14c2qcwB_
93.6 18 PDB header:signaling protein
Chain: B: PDB Molecule:bone morphogenetic protein 6;
PDBTitle: crystal structure of bone morphogenetic protein-6 (bmp-6)
15d1pdga_
92.6 19 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Platelet-derived growth factor-like
16c1agqB_
92.1 19 PDB header:growth factor
Chain: B: PDB Molecule:glial cell-derived neurotrophic factor;
PDBTitle: glial cell-derived neurotrophic factor from rat
17c2xv7A_
92.1 19 PDB header:hormone
Chain: A: PDB Molecule:vascular endothelial growth factor d;
PDBTitle: crystal structure of vascular endothelial growth factor d
18c3mjkE_
91.4 23 PDB header:hormone
Chain: E: PDB Molecule:platelet-derived growth factor subunit a;
PDBTitle: structure of a growth factor precursor
19d1ktza_
90.7 16 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Transforming growth factor (TGF)-beta
20d1agqa_
90.5 19 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Transforming growth factor (TGF)-beta
21c3mjgB_
not modelled 90.3 21 PDB header:hormone/transferase
Chain: B: PDB Molecule:platelet-derived growth factor subunit b;
PDBTitle: the structure of a platelet derived growth factor receptor complex
22c2gnnD_
not modelled 89.5 21 PDB header:hormone/growth factor
Chain: D: PDB Molecule:vascular endothelial growth factor homolog;
PDBTitle: crystal structure of the orf virus nz2 variant of vegf-e
23c2c7wB_
not modelled 89.4 21 PDB header:growth factor
Chain: B: PDB Molecule:vascular endothelial growth factor b precursor;
PDBTitle: crystal structure of human vascular endothelial growth2 factor-b: identification of amino acids important for3 angiogeninc activity
24d2tgia_
not modelled 88.6 16 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Transforming growth factor (TGF)-beta
25d1fzva_
not modelled 88.6 18 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Platelet-derived growth factor-like
26c1fzvB_
not modelled 88.6 18 PDB header:hormone/growth factor
Chain: B: PDB Molecule:placenta growth factor;
PDBTitle: the crystal structure of human placenta growth factor-12 (plgf-1), an angiogenic protein at 2.0a resolution
27d1klaa_
not modelled 88.5 16 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Transforming growth factor (TGF)-beta
28c2vweB_
not modelled 88.2 21 PDB header:immune system
Chain: B: PDB Molecule:vascular endothelial growth factor b;
PDBTitle: crystal structure of vascular endothelial growth factor-b2 in complex with a neutralizing antibody fab fragment
29c2gnnA_
not modelled 88.0 21 PDB header:hormone/growth factor
Chain: A: PDB Molecule:vascular endothelial growth factor homolog;
PDBTitle: crystal structure of the orf virus nz2 variant of vegf-e
30c3v6bA_
not modelled 87.2 22 PDB header:hormone/signaling protein
Chain: A: PDB Molecule:vegf-e;
PDBTitle: vegfr-2/vegf-e complex structure
31d1wq9a_
not modelled 87.2 14 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Platelet-derived growth factor-like
32c3rjrD_
not modelled 87.2 16 PDB header:cytokine
Chain: D: PDB Molecule:transforming growth factor beta-1;
PDBTitle: crystal structure of pro-tgf beta 1
33d1tgja_
not modelled 86.4 13 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Transforming growth factor (TGF)-beta
34c2gnnB_
not modelled 82.4 23 PDB header:hormone/growth factor
Chain: B: PDB Molecule:vascular endothelial growth factor homolog;
PDBTitle: crystal structure of the orf virus nz2 variant of vegf-e
35c3v2aA_
not modelled 81.7 18 PDB header:hormone/signaling protein
Chain: A: PDB Molecule:vascular endothelial growth factor a;
PDBTitle: vegfr-2/vegf-a complex structure
36d1fltv_
not modelled 81.7 18 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Platelet-derived growth factor-like
37c2gnnC_
not modelled 80.1 21 PDB header:hormone/growth factor
Chain: C: PDB Molecule:vascular endothelial growth factor homolog;
PDBTitle: crystal structure of the orf virus nz2 variant of vegf-e
38d1wq8a_
not modelled 69.3 16 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Platelet-derived growth factor-like
39d2fiya1
not modelled 64.2 22 Fold:FdhE-like
Superfamily:FdhE-like
Family:FdhE-like
40c2x1wC_
not modelled 54.5 23 PDB header:hormone/signaling protein
Chain: C: PDB Molecule:vascular endothelial growth factor c;
PDBTitle: crystal structure of vegf-c in complex with domains 2 and 32 of vegfr2
41d1n26a1
not modelled 27.8 64 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Immunoglobulin
Family:I set domains
42c2nswA_
not modelled 17.3 60 PDB header:signaling protein
Chain: A: PDB Molecule:mating pheromone en-2;
PDBTitle: nmr solution structure of the pheromone en-2
43d1hcna_
not modelled 16.5 25 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Gonadodropin/Follitropin
44d1nuia2
not modelled 13.3 28 Fold:Rubredoxin-like
Superfamily:Zinc beta-ribbon
Family:DNA primase zinc finger
45c1tx6J_
not modelled 12.0 18 PDB header:hydrolase/protein binding
Chain: J: PDB Molecule:bowman-birk type trypsin inhibitor;
PDBTitle: trypsin:bbi complex
46d1mr1c_
not modelled 11.8 25 Fold:SAND domain-like
Superfamily:SAND domain-like
Family:SMAD4-binding domain of oncoprotein Ski
47c3facE_
not modelled 11.7 15 PDB header:unknown function
Chain: E: PDB Molecule:putative uncharacterized protein;
PDBTitle: crystal structure of rhodobacter sphaeroides protein2 rsp_2168. northeast structural genomics target rhr83.
48c1tdhA_
not modelled 11.0 36 PDB header:hydrolase
Chain: A: PDB Molecule:nei endonuclease viii-like 1;
PDBTitle: crystal structure of human endonuclease viii-like 1 (neil1)
49d1k81a_
not modelled 10.8 21 Fold:Zinc-binding domain of translation initiation factor 2 beta
Superfamily:Zinc-binding domain of translation initiation factor 2 beta
Family:Zinc-binding domain of translation initiation factor 2 beta
50d1m4ua_
not modelled 9.2 29 Fold:Cystine-knot cytokines
Superfamily:Cystine-knot cytokines
Family:Noggin
51c1neeA_
not modelled 9.1 21 PDB header:translation
Chain: A: PDB Molecule:probable translation initiation factor 2 beta
PDBTitle: structure of archaeal translation factor aif2beta from2 methanobacterium thermoautrophicum
52c2e9hA_
not modelled 7.9 22 PDB header:translation
Chain: A: PDB Molecule:eukaryotic translation initiation factor 5;
PDBTitle: solution structure of the eif-5_eif-2b domain from human2 eukaryotic translation initiation factor 5
53c2dcuB_
not modelled 7.9 28 PDB header:translation
Chain: B: PDB Molecule:translation initiation factor 2 beta subunit;
PDBTitle: crystal structure of translation initiation factor aif2betagamma2 heterodimer with gdp
54d2cora1
not modelled 7.2 45 Fold:Glucocorticoid receptor-like (DNA-binding domain)
Superfamily:Glucocorticoid receptor-like (DNA-binding domain)
Family:LIM domain
55c3h32A_
not modelled 7.0 29 PDB header:blood clotting
Chain: A: PDB Molecule:fibrinogen alpha chain;
PDBTitle: crystal structure of d-dimer from human fibrin complexed with gly-his-2 arg-pro-tyr-amide
56d1p8ba_
not modelled 6.9 36 Fold:Knottins (small inhibitors, toxins, lectins)
Superfamily:omega toxin-like
Family:Albumin 1
57c3cw2M_
not modelled 6.8 24 PDB header:translation
Chain: M: PDB Molecule:translation initiation factor 2 subunit beta;
PDBTitle: crystal structure of the intact archaeal translation2 initiation factor 2 from sulfolobus solfataricus .
58d2cona1
not modelled 6.8 35 Fold:Rubredoxin-like
Superfamily:NOB1 zinc finger-like
Family:NOB1 zinc finger-like
59c2h43A_
not modelled 6.4 29 PDB header:blood clotting
Chain: A: PDB Molecule:fibrinogen alpha chain;
PDBTitle: crystal structure of human fragment d complexed with ala-his-arg-pro-2 amide
60d1gsma1
not modelled 6.3 31 Fold:Immunoglobulin-like beta-sandwich
Superfamily:Immunoglobulin
Family:I set domains
61d2fufa1
not modelled 5.9 17 Fold:Origin of replication-binding domain, RBD-like
Superfamily:Origin of replication-binding domain, RBD-like
Family:The origin DNA-binding domain of SV40 T-antigen
62c1n73A_
not modelled 5.7 43 PDB header:blood clotting
Chain: A: PDB Molecule:fibrin alpha-1 chain;
PDBTitle: fibrin d-dimer, lamprey complexed with the peptide ligand: gly-his-2 arg-pro-amide
63d1weqa_
not modelled 5.5 40 Fold:FYVE/PHD zinc finger
Superfamily:FYVE/PHD zinc finger
Family:PHD domain
64d1tdha3
not modelled 5.5 36 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
65d1gpua2
not modelled 5.4 63 Fold:Thiamin diphosphate-binding fold (THDP-binding)
Superfamily:Thiamin diphosphate-binding fold (THDP-binding)
Family:TK-like Pyr module
66c1re3A_
not modelled 5.4 29 PDB header:blood clotting
Chain: A: PDB Molecule:fibrinogen alpha/alpha-e chain;
PDBTitle: crystal structure of fragment d of bbetad398a fibrinogen with the2 peptide ligand gly-his-arg-pro-amide
67d1ju8a_
not modelled 5.3 45 Fold:Knottins (small inhibitors, toxins, lectins)
Superfamily:omega toxin-like
Family:Albumin 1
68c2o01I_
not modelled 5.3 40 PDB header:photosynthesis
Chain: I: PDB Molecule:photosystem i reaction center subunit viii;
PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution
69c2wseI_
not modelled 5.3 40 PDB header:photosynthesis
Chain: I: PDB Molecule:photosystem i reaction center subunit viii;
PDBTitle: improved model of plant photosystem i
70c3lw5I_
not modelled 5.3 40 PDB header:photosynthesis
Chain: I: PDB Molecule:photosystem i reaction center subunit viii;
PDBTitle: improved model of plant photosystem i

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