Email l.a.kelley@imperial.ac.uk Description A2A5H7 Date Wed Jul 10 14:29:34 BST 2013 Unique Job ID 28d09187c4d06d94 Sequence MKPSWFPCLV ... Download FASTA

Summary

Top model

Image coloured by rainbow N → C terminus Model dimensions (Å): X:17.486 Y:20.512 Z:22.226 Close Jmol

Model (left) based on template c2kyjA_ Top template information PDB header:toxin Chain: A: PDB Molecule:litx; PDBTitle: structure of the scorpion toxin u1-liotoxin-lw1a Confidence and coverage Confidence: 19.4% Coverage: 15% 12 residues ( 15% of your sequence) have been modelled with 19.4% 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 ( 16%) Alpha helix ( 82%) Beta strand ( 0%)

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 2kyj chain A Region: 49 - 60 Aligned: 12 Modelled: 12 Confidence: 19.4% Identity: 42% PDB header:toxin Chain: A: PDB Molecule:litx; PDBTitle: structure of the scorpion toxin u1-liotoxin-lw1a Phyre2 PDB 2qj2 chain A domain 1 Region: 42 - 65 Aligned: 24 Modelled: 24 Confidence: 16.3% Identity: 33% Fold: Hairpin loop containing domain-like Superfamily: Hairpin loop containing domain-like Family: Hairpin loop containing domain Phyre2 PDB 2lur chain A Region: 55 - 69 Aligned: 15 Modelled: 15 Confidence: 15.3% Identity: 40% PDB header:plant protein Chain: A: PDB Molecule:kalata; PDBTitle: nmr solution structure of kb1[ghrw;23-28] Phyre2 PDB 1zue chain A domain 1 Region: 65 - 70 Aligned: 6 Modelled: 6 Confidence: 13.9% Identity: 83% Fold: Defensin-like Superfamily: Defensin-like Family: Defensin Phyre2 PDB 2wwb chain C Region: 6 - 21 Aligned: 16 Modelled: 16 Confidence: 12.9% Identity: 25% PDB header:ribosome Chain: C: PDB Molecule:protein transport protein sec61 subunit beta; PDBTitle: cryo-em structure of the mammalian sec61 complex bound to the2 actively translating wheat germ 80s ribosome Phyre2 PDB 3c9a chain D Region: 59 - 77 Aligned: 19 Modelled: 19 Confidence: 12.5% Identity: 16% PDB header:hormone/signaling protein Chain: D: PDB Molecule:protein spitz; PDBTitle: high resolution crystal structure of argos bound to the egf2 domain of spitz Phyre2 PDB 1ata chain A Region: 55 - 69 Aligned: 13 Modelled: 15 Confidence: 11.6% Identity: 54% Fold: Serine protease inhibitors Superfamily: Serine protease inhibitors Family: ATI-like Phyre2 PDB 4geh chain B Region: 12 - 27 Aligned: 16 Modelled: 16 Confidence: 10.6% Identity: 25% PDB header:protein binding/transferase Chain: B: PDB Molecule:serine/threonine-protein kinase mst4; PDBTitle: crystal structure of mst4 dimerization domain complex with pdcd10 Phyre2 PDB 1oh4 chain A Region: 66 - 81 Aligned: 16 Modelled: 16 Confidence: 10.5% Identity: 31% Fold: Galactose-binding domain-like Superfamily: Galactose-binding domain-like Family: Family 27 carbohydrate binding module, CBM27 Phyre2 PDB 3zq7 chain A Region: 16 - 41 Aligned: 26 Modelled: 26 Confidence: 8.4% Identity: 31% PDB header:transcription Chain: A: PDB Molecule:kdp operon transcriptional regulatory protein kdpe; PDBTitle: the structure of dna-binding domain of response regulator2 from escherichia coli k-12 Phyre2 PDB 1h8p chain B Region: 58 - 70 Aligned: 13 Modelled: 13 Confidence: 7.8% Identity: 23% PDB header:phosphorylcholine-binding protein Chain: B: PDB Molecule:seminal plasma protein pdc-109; PDBTitle: bull seminal plasma pdc-109 fibronectin type ii module Phyre2 PDB 2e4w chain A Region: 39 - 66 Aligned: 28 Modelled: 28 Confidence: 7.7% Identity: 25% PDB header:signaling protein Chain: A: PDB Molecule:metabotropic glutamate receptor 3; PDBTitle: crystal structure of the extracellular region of the group ii2 metabotropic glutamate receptor complexed with 1s,3s-acpd Phyre2 PDB 1t0w chain A Region: 59 - 69 Aligned: 11 Modelled: 11 Confidence: 7.6% Identity: 55% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Plant lectins/antimicrobial peptides Family: Hevein-like agglutinin (lectin) domain Phyre2 PDB 2lds chain A Region: 49 - 59 Aligned: 11 Modelled: 11 Confidence: 7.0% Identity: 36% PDB header:toxin Chain: A: PDB Molecule:insecticidal toxin lait1; PDBTitle: solution structure of a short-chain lait1 from the venom of scorpion2 liocheles australasiae Phyre2 PDB 3w8h chain B Region: 12 - 27 Aligned: 16 Modelled: 16 Confidence: 6.4% Identity: 31% PDB header:protein binding/transferase Chain: B: PDB Molecule:serine/threonine-protein kinase 25; PDBTitle: crystal structure of ccm3 in complex with the c-terminal regulatory2 domain of stk25 Phyre2 PDB 1nra chain A Region: 66 - 76 Aligned: 11 Modelled: 11 Confidence: 6.3% Identity: 36% Fold: Knottins (small inhibitors, toxins, lectins) Superfamily: Scorpion toxin-like Family: Long-chain scorpion toxins Phyre2 PDB 2zxj chain B Region: 16 - 42 Aligned: 27 Modelled: 27 Confidence: 6.3% Identity: 26% PDB header:transcription Chain: B: PDB Molecule:transcriptional regulatory protein walr; PDBTitle: crystal structure of yycf dna-binding domain from staphylococcus2 aureus Phyre2 PDB 1edg chain A Region: 35 - 43 Aligned: 9 Modelled: 9 Confidence: 6.2% Identity: 44% Fold: TIM beta/alpha-barrel Superfamily: (Trans)glycosidases Family: beta-glycanases Phyre2 PDB 2k21 chain A Region: 5 - 61 Aligned: 57 Modelled: 57 Confidence: 6.0% Identity: 14% PDB header:membrane protein Chain: A: PDB Molecule:potassium voltage-gated channel subfamily e PDBTitle: nmr structure of human kcne1 in lmpg micelles at ph 6.0 and2 40 degree c Phyre2 PDB 4dwc chain A Region: 60 - 64 Aligned: 5 Modelled: 5 Confidence: 5.8% Identity: 80% PDB header:viral protein Chain: A: PDB Molecule:e(rns) glycoprotein; PDBTitle: crystal structure of the glycoprotein erns from the pestivirus bvdv-12 in complex with zn ions Phyre2 1 c2kyjA_ 2 d2qj2a1 3 c2lurA_ 4 d1zuea1 5 c2wwbC_ 6 c3c9aD_ 7 d1ataa_ 8 c4gehB_ 9 d1oh4a_ 10 c3zq7A_ 11 c1h8pB_ 12 c2e4wA_ 13 d1t0wa_ 14 c2ldsA_ 15 c3w8hB_ 16 d1nraa_ 17 c2zxjB_ 18 d1edga_ 19 c2k21A_ 20 c4dwcA_ 21 22

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