Email l.a.kelley@imperial.ac.uk Description C6Y4A2 Date Sun Jul 8 11:45:04 BST 2012 Unique Job ID 91e5152cf7bdb90c

Summary

Top model

Image coloured by rainbow N → C terminus Close Jmol

Model (left) based on template c2vofB_ Top template information PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-binding component 3; PDBTitle: structure of mouse a1 bound to the puma bh3-domain Confidence and coverage Confidence: 13.6% Coverage: 12% 11 residues ( 12% of your sequence) have been modelled with 13.6% confidence by the single highest scoring template. You may wish to submit your sequence to Phyrealarm. This will automatically scan your sequence every week for new potential templates as they appear in the Phyre2 library. Please note: You must be registered and logged in to use Phyrealarm. 3D viewing Interactive 3D view in Jmol

Sequence analysis

Secondary structure and disorder prediction

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

PDB 2vof chain B Region: 13 - 23 Aligned: 11 Modelled: 11 Confidence: 13.6% Identity: 55% PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-binding component 3; PDBTitle: structure of mouse a1 bound to the puma bh3-domain Phyre2 PDB 2roc chain B Region: 13 - 23 Aligned: 11 Modelled: 11 Confidence: 12.5% Identity: 55% PDB header:apoptosis Chain: B: PDB Molecule:bcl-2-binding component 3; PDBTitle: solution structure of mcl-1 complexed with puma Phyre2 PDB 2cwo chain D Region: 11 - 20 Aligned: 10 Modelled: 10 Confidence: 10.4% Identity: 60% PDB header:rna binding protein Chain: D: PDB Molecule:rna silencing suppressor; PDBTitle: crystal structure of rna silencing suppressor p21 from beet yellows2 virus Phyre2 PDB 3mmi chain B Region: 8 - 27 Aligned: 20 Modelled: 20 Confidence: 8.7% Identity: 25% PDB header:motor protein Chain: B: PDB Molecule:myosin-4; PDBTitle: crystal structure of the globular tail of myo4p Phyre2 PDB 1qzm chain A Region: 9 - 20 Aligned: 12 Modelled: 12 Confidence: 7.9% Identity: 33% Fold: P-loop containing nucleoside triphosphate hydrolases Superfamily: P-loop containing nucleoside triphosphate hydrolases Family: Extended AAA-ATPase domain Phyre2 PDB 1h5o chain A Region: 36 - 41 Aligned: 6 Modelled: 6 Confidence: 6.9% Identity: 100% Fold: Defensin-like Superfamily: Defensin-like Family: Myotoxin Phyre2 PDB 1x37 chain A Region: 9 - 20 Aligned: 12 Modelled: 12 Confidence: 6.8% Identity: 33% PDB header:hydrolase Chain: A: PDB Molecule:atp-dependent protease la 1; PDBTitle: structure of bacillus subtilis lon protease ssd domain Phyre2 PDB 4aco chain A Region: 9 - 20 Aligned: 11 Modelled: 12 Confidence: 6.5% Identity: 36% PDB header:dna binding protein Chain: A: PDB Molecule:centromere dna-binding protein complex cbf3 subunit a; PDBTitle: structure of the budding yeast ndc10 n-terminal domain Phyre2 PDB 3o7v chain X Region: 24 - 52 Aligned: 28 Modelled: 29 Confidence: 6.4% Identity: 29% PDB header:rna binding protein/rna Chain: X: PDB Molecule:piwi-like protein 1; PDBTitle: crystal structure of human hiwi1 (v361m) paz domain (residues 277-399)2 in complex with 14-mer rna (12-bp + 2-nt overhang) containing 2'-och33 at its 3'-end Phyre2 PDB 3ktm chain B Region: 12 - 33 Aligned: 22 Modelled: 22 Confidence: 6.2% Identity: 41% PDB header:cell adhesion, signaling protein Chain: B: PDB Molecule:amyloid beta a4 protein; PDBTitle: structure of the heparin-induced e1-dimer of the amyloid precursor2 protein (app) Phyre2 PDB 2f6h chain X Region: 8 - 20 Aligned: 13 Modelled: 13 Confidence: 6.1% Identity: 38% PDB header:structural protein Chain: X: PDB Molecule:myosin-2; PDBTitle: myosin v cargo binding domain Phyre2 PDB 2vof chain D Region: 15 - 23 Aligned: 9 Modelled: 9 Confidence: 5.4% Identity: 56% PDB header:apoptosis Chain: D: PDB Molecule:bcl-2-binding component 3; PDBTitle: structure of mouse a1 bound to the puma bh3-domain Phyre2 PDB 3sqi chain A Region: 10 - 24 Aligned: 14 Modelled: 15 Confidence: 5.2% Identity: 21% PDB header:dna binding protein/dna Chain: A: PDB Molecule:klla0e03807p; PDBTitle: dna binding domain of ndc10 Phyre2 1 c2vofB_ 2 c2rocB_ 3 c2cwoD_ 4 c3mmiB_ 5 d1qzma_ 6 d1h5oa_ 7 c1x37A_ 8 c4acoA_ 9 c3o7vX_ 10 c3ktmB_ 11 c2f6hX_ 12 c2vofD_ 13 c3sqiA_

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 Disclaimer Terms and Conditions	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