PASS2
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Superfamily Details

Superfamily summary
Superfamily Name:  PKD domain
Class Name:  All beta proteins
Fold Name:  Immunoglobulin-like beta-sandwich
Number of Members:  3
Average Size: 
Members
SCOP ID Name Source
d1b4ra- Polycystein-1, PKD-1 Human (Homo sapiens) [TaxId: 9606]
d1l0qa1 Surface layer protein Archaeon Methanosarcina mazei [TaxId: 2209]
d1wgoa- VPS10 domain-containing receptor SorCS2 Human (Homo sapiens) [TaxId: 9606]

Alignment Based On Similarities In Structural Features using Comparer

                             10        20        30        40        50  
d1b4ra-  (   8 )                                  Atlvgphg--plasgqlAaF
d1l0qa1  ( 302 )                            pvyPs-AdFksnitsgyiflsepVqF
d1wgoa-  (   1 )    gssgssgceggvdmqqsqvqlqcpltpPrglqvsiqgeavavrpgedvlF
                                                    bb             bbb

                             60        70        80        90        100 
d1b4ra-  (  26 )    hia-aplpvt--atrWdFgDgsaevdaagp-----aasHrYvlpgryhvt
d1l0qa1  ( 327 )    tDlSk--dAt--ewkWdFgdgs-sskk--q-----nPthtYsetgiytVr
d1wgoa-  (  51 )    vvrqeqgdvlttkYqvdlgdgf-kamyvnltltgepirhrYespgiyrvs
                    bb          bbbbb      bb            bb       bbbb

                             110       120       
d1b4ra-  (  68 )    Avlalgagsallgtdvqvea         
d1l0qa1  ( 365 )    LtVsnsngtdsqistVnVvlk--gsptps
d1wgoa-  ( 100 )    vrAentaghdeAvlfvqvsgpssg     
                    bbbb    bbbbbbbb             

solvent inaccessible: UPPER CASE X
solvent accesible: lower case x
alpha helix: red x
beta strand: blue x
3 - 10 helix: maroon x
hydrogen bond to main chain amide: bold x
hydrogen bond to mainchain carbonyl: underline x
disulphide bond: cedilla ç
positive phi: italic x

Jmol view

Jmol Model View
Jmol Command prompt
Response Logs

Tree based on RMSD between structures

Matrices

1. Percentage Identity Matrix  [View | Download]
2. Distance Matrix  [View | Download]

PCA based on sequence identity

1. PCA  [View]
2. Plot file  [Download]

CUSP Results

CUSP Result   [View | Download]

Alistat - Alignment Statistics

Alignment Statistics  [Download]

SMotif - Conserved Structural Motifs

SMotif Result   [View | Download]

MeanRMS

MeanRMS  [Download]