PASS2
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Superfamily Details

Superfamily summary
Superfamily Name:  RuBisCo, C-terminal domain
Class Name:  Alpha and beta proteins (a/b)
Fold Name:  TIM beta/alpha-barrel
Number of Members:  4
Average Size: 
Members
SCOP ID Name Source
d5ruba1 Ribulose 1,5-bisphosphate carboxylase-oxygenase Rhodospirillum rubrum [TaxId: 1085]
d1ykwa1 Ribulose 1,5-bisphosphate carboxylase-oxygenase Chlorobium tepidum [TaxId: 1097]
d1wdda1 Ribulose 1,5-bisphosphate carboxylase-oxygenase Rice (Oryza sativa) [TaxId: 4530]
d2d69a1 Ribulose 1,5-bisphosphate carboxylase-oxygenase Archaeon Pyrococcus horikoshii [TaxId: 53953]

Alignment Based On Similarities In Structural Features using Comparer

                             10        20        30        40        50  
d1wdda1  ( 151 )      PPhGiqvErdkLnky---grPLLGCtIkpklglsaknYGraCyeCLrg
d1ykwa1  ( 146 )    eGPkfGIegLRdiLnAh---grPIFFGvVkpniglspgeFaeiAyqSWlG
d2d69a1  ( 134 )    kGPqfGVqgIRefMgvk---drPLTATvPkpkmgwsveeYAeiAyeLWsg
d5ruba1  ( 138 )     gPsvnIsaLWkvLgrpevdGgLVVGtiIkpklglrpkpFAeaChafWl-
                          aaaaaaaa         bbbb         aaaaaaaaaaaaa 

                             60        70        80        90        100 
d1wdda1  ( 196 )    gLDFT-DDenVnsqpfMrwrdRFvfCAeAIykSqaetgeiKGHYLNAtAg
d1ykwa1  ( 193 )    gLDIAKDDemLadvtwSsIeeRAahLGkarrkAeaetgepKIYLANItd-
d2d69a1  ( 181 )    gIDLLKDDenFtsfpfNrFeeRVrkLYrvrdrVeaetgetKEYLINItg-
d5ruba1  ( 186 )    GGDFIKnDepqgnqpfaplrdtIalVAdAMrrAqdetgeaKLFSAnItad
                       bbb            aaaaaaaaaaaaaaaaaaa    bbbbb    

                             110       120       130       140       150 
d1wdda1  ( 246 )    tceeMikrAvfArel-----gVpIVMHDYLtggftaNtsLAhyCrdngLL
d1ykwa1  ( 242 )    evdsLmekHdvAvrn-----gAnALLInAlpVglsAVrmLSnyT---qvP
d2d69a1  ( 230 )    pvniMekrAemVane-----gGqYVMIDIvvagwsaLqyMRevTedlgLA
d5ruba1  ( 236 )    dpfeIiarGeyVletFgeNashVALLVdGyvagaaAIttArrrfp--dnF
                     aaaaaaaaaaaaaa        bbbbbaaaa aaaaaaaaaa       

                             160       170       180       190       200 
d1wdda1  ( 291 )    LHIhramhavidrqk-nhgmhFrvLAkaLRmsGGDHIhAgTvvGkleger
d1ykwa1  ( 284 )    LIGhfpfiasfsrme-kygihskvmTklQRlaGLDAVIMpGFgdrvmtpe
d2d69a1  ( 275 )    IHAhramhaafTrnp-rhgitMlaLAkaARmiGVDQIhTgTaVgkmagny
d5ruba1  ( 284 )    LHYhraghgavTspqskrgytafvHCkmARlqGASGIhTgts--------
                    bbbb    aaaa         aaaaaaaaaaa   bbb           a

                             210       220       230       240       250 
d1wdda1  ( 340 )    eMTlGfVdLLrddfiekdrargIfftqdwvsmpGVIPVAsggIHVwHMPa
d1ykwa1  ( 333 )    eeVlenvieCtkpmg---------------rikpCLPVPgGsDSAltLqt
d2d69a1  ( 324 )    eeIkrINdfLls---------------kwehirpVFPVasggLhPglMpe
d5ruba1  ( 335 )    -sdraiAyMLtqdeaqGpf-----yrqsWggmkaCTPIIsggmnALrMpg
                    aaaaaaaaaaa                        bbbbb       aaa

                             260       270       280       290       300 
d1wdda1  ( 390 )    LTeIFg-ddSVLQFGgGTlgHpwgnapGAaANrvALeaCvqarnegrdLa
d1ykwa1  ( 368 )    VyekVgnvdFGFvPgrGVfgHpmgpkAGAkSIrqAWeAIeq---------
d2d69a1  ( 359 )    LirlFg-kdLVIqAGggVmgHpdgpraGAkALrdAIdAaie---------
d5ruba1  ( 379 )    fFenLgnAnVIlTAgggaFgHidgpvaGArSLrqAWqAwrd---------
                    aaaaa     bbb           aaaaaaaaaaaaaaaaa         

                             310       320       330       340 
d1wdda1  ( 439 )    regneiIrsackwSpeLaaACeiwkaikfefepvdkl    
d1ykwa1  ( 409 )    ---gisietwAethpeLqamvdq                  
d2d69a1  ( 399 )    ---gvdldekaksSpeLkkslrevglsk--------a    
d5ruba1  ( 420 )    ---gvpvldyArehkeLarAFeSfpgdAdqiypgWrkalgv
                          aaaaa   aaaaaaaaa                  

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]