• Backbone structures are obtained using ProteinViewer, where N-terminal is colored red and C-terminal blue.
• Click the images to view larger image.
• Click PDB IDs to view the corresponding PDB file
• See the bottom for explanation of the DSSP codes and the 5-tile codes. 

(1) Retinol-Binding Protein (1hbq) and Retinoic Acid-Binding Protein (1cbs)

			"From the classical fold definition standpoint, such a difference warrants placement of 1hbq and 1cbs in two different folds. The following similarities, however, indicate homology between these proteins. First, the sutructural similarity in the common regions is pronounced, which includes conserved length and tilt of the beta-strands. Second, both proteins are functionally similar and bind lipids inside the beta-barrel." (Grishin, 2001)
1hbq (Res19-142)	1cbs (Res3-137)

1hbq AGTWYAMAKKDPEG         LF            LQDNIVAEFSVDENG QMSATAK  GRVRLLNNWDVC  ADMVGT  FTDT code G00000R000000R         00            001R00000000QBR 0000000  00000QBR0000  000000  0000 LCS   00000R000   R         00            00  00000000  R 0000000  00000   0000  000000  0000 code  00000R000   RQAAAAAABR00QAAAAAAAAAAB00  00000000  RG0000000QG00000   0000RG000000QB0000 1cbs  GNWKIIRSE   NFEELLKVLGVNVMLRKIAVAAASKP  AVEIKQEG  DTFYIKTSTTVRTTEI   NFKVGEEFEEQTVDGRPC 1hbq EDPAKFKMKYWGVASFLQKGNDDHWIIDTDYETFAVQYSCRLLN LDGTCADSYSFVFARD code RGQBG0000000RGQBG000000000R00RQG00000000R000 QBRG0R00000000RG LCS        000000R QBG0000000  R00   00000000 000 QBR 0 00000000RG code       000000R0QBG0000000  R00   00000000 0000QBR 0 00000000RG0000000 1cbs       KSLVKWESENKMVCEQKL  LKG   EGPKTSWT RELTNDG E LILTMTADDVVCTRVYV *RATIO :  lcs/trimmed_seq_a = 0.783 (=   94/  120), lcs/trimmed_seq_b = 0.718 (=   94/  131)

Structural alignment by ComSubstruct

DSSP lLLEEEEEEEEELLLL...............LLLLEEEEEEEEELLlLLEEEEEEEEeellllleeEEEEEEE..................eEEL 1hbq rFAGTWYAMAKKDPEG...............LFLQDNIVAEFSVDEnGQMSATAKGRvrllnnwdvCADMVGT..................fTDT       | | |        |                         | 1cbs .FSGNWKIIRSENFEEllkvlgvnvmlrkiaVAAASKPAVEIKQEG.DTFYIKTSTT.........VRTTEINfkvgeefeeqtvdgrpcksLVK DSSP .LLEEEEEEEEELHHHhhhhllllhhhhhhhHHHHLLLEEEEEEEL.LEEEEEEELL.........LLEEEEEeelllleeeellllleeeeEEE DSSP LL...lLEEEeeeeellllllleeEEEEEeEELLLLEEEEEEEEEEllllleeEEEEEEEELLll 1hbq ED...pAKFKmkywgvasflqkgnDDHWIiDTDYETFAVQYSCRLLnldgtcaDSYSFVFARDps                                                                |  | 1cbs WEsenkMVCE....qkllkgegpkTSWTR.ELTNDGELILTMTADD.......VVCTRVYVRE.. DSSP EEelleEEEE....eeelllllllEEEEE.EELLLLLEEEEEEELL.......EEEEEEEEEL.. *Z-score 6.7  AR 87  RMSD 2.8A  SI 8%

Structural alignment by DaliLite

(2) Active alpha1-Antitrypsin (1kct) and Latent PAI-1 (1c5g)

			"Serpins fold into a metastable structure that can exist in at least two drastically different conformations. Such structures may arise in protein evolution as a consequence of substitutions/indels/. Since these metastable proteins still fold and might be functional, they will not be eliminated. Further mutations may result in the fixation of one of the conformations and cause a change of fold" (Grishin, 2001)
1kct	1c5g

1kct  TFNKITPNLAEFAFSLYRQLAH    QSNSTN I FFSPVSIAAA       FAMLSLG AKGDT HDEILEGLN FNLTE IPEAQIHEGF code  QAAB1QAA9AAAAAAAAAAAAI    BGRG00 0 000RHBHBHQ       AAAARHB 000RH AAAGQAABR 00QAB 001AAHQAAA LCS   QAA   AA AAAAAAAAAAAA     B   00 0 000      Q       AAAA HB 00    AAA  AABR 0 Q B 0  AA  AAA code 0QAA   AA AAAAAAAAAAAAAAAAAB   00R0R0000     QAAAAAAAAAAA HBG00QAAAAAA  AABRG0 Q BG0RQAA  AAA 1c5g HPPS   YV AHLASDFGVRVFQQVAQA   SKDRNVVFS     PYGVASVLAMLQ LTTGGETQQQIQ  AAMGFK I DDKGMAP  ALR 1kct QELLRTL  NQ  P DSQLQLTTGNGLFLSEGLKLV   DKFLEDVKKLYH SEAFTVNF  GDTE    EAKKQINDYVEKGTQGKIVD code AAAB1AA  00  R 001B00000RR0000RG0O00   QAAAAHAAB0RR 0000000Q  QG1H    AAABG1QAAAAB1RR01BR0 LCS  AAA  AA  0   R 00  00000  0000  0 00   QAAAA AA  RR 000000 Q  Q       AAA    AAAAB RR   R0 code AAA  AAAB0QABRG00  00000  0000QB0 0000RQAAAA AAG RRG000000 QABQAAAAAAAAAA    AAAAB RR   R00 1c5g HLY  KELMGPWNKDEI  STTDA  IFVQRDL KLVQGFMPHF FRL FRSTVKQVD FSEVERARFIINDW    VKTHT KG   MIS 1kct L VKE   LD   RDTVFALVNYIFFKG KWERPFEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKKLSSWVLLMKYLG code R G30   00   R000R0000000000 00QB000QABG00000000QABR0R0R000000R0R0000QBR0G0000000O0 LCS  R G 0   00   R000 0000000000 00  00 QABG00000      R R0R000000 0 0000   0 0000000 0 code RRG 0QAB00QBGR000 0000000000R00  00 QABG00000      R R0R000000 0 0000   0 0000000 000QB 1c5g NLL GKGAVDQLTRLVL VNALYFNGQWKTP  FP DSSTHRRLF      H KSDGSTVSV P MMAQ   T NKFNYTE FTTPD 1kct NATAIFFLPDE  G KLQ     HL ENE       LTHDIITKFL ENE DRRSASLHLPKLSITGTYD LK    S  VLGQLG   IT KVFSN code R0000000000  R 001     R9 BGR       00QAAAAAAA G00 000000000001R000000 QA    B  1QAAB1   R0 QAB0R LCS  R0000000000  R 00      R  BG        00QAAAAAAA G00 00000000000  000000 QA    B  1 AAB    R0 QA 0R code R0000000000QBRR00000000R0QBG0QAAAAAB00QAAAAAAAAG00O00000000000  000000RQAAAAAB001 AABGQ80R0RQAG0RB000 1c5g GHYYDILELPYHGDTLSMFIAAPYEKEVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFS  LETEVDLRKPLENLGMT DMFRQFQADFTSLSDQEPL 1kct GAD           LSGVTEEAPLKLSKAVHKAVLTIDEKGTEAAGAMFLEAIPMSIPPEVKFNKPFVFL MIEQNT   K     SPLFMGKVVNPT code 00R           QAAB0RGR3000R0000R0000G00001R0RR1QAQAAABJ0RRG0RRRRG00000 000QB0   R     03R0000OR0QA LCS  00R           Q  B0    000 0000 0000 0000  0           0   0     00000 000  0   R     0 R0000  0 code 00R00000000000Q  B0    000 0000 0000 0000  0           0   0     000003000  0000R1ABR00 R0000  00 1c5g HVAQALQKVKIEVNE  SG    TVA SSST AVIV SARM  A           P   E     EIIMDRPFL  FVVRHNPTGTV LFMGQ  VM *RATIO :  lcs/trimmed_seq_a = 0.690 (=  256/  371), lcs/trimmed_seq_b = 0.683 (=  256/  375)

Structural alignment by ComSubstruct

DSSP .LLLLLLLLLLLLLLHHHHHLLLLLLLLLLLEEELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLllllLLLLLLLLL 1kct .HPTFNKITPNLAEFAFSLYRQLAHQSNSTNIFFSPVSIAAAFAMLSLGAKGDTHDEILEGLNFNlteiPEAQIHEGF       |            |      | |  |   |  |||   |   ||| |   | |   |     | 1c5g vHHPPSYVAHLASDFGVRVFQQVAQASKDRNVVFSPYGVASVLAMLQLTTGGETQQQIQAAMGFK...iDDKGMAPAL DSSP lLLHHHHHHHHHHHHHHHHHHHHHHLLLLLLLEELHHHHHHHHHHLLLLLLHHHHHHHHHHHLLL...lLLLLHHHHH DSSP LLLLLLLLLLLLLLLLLLEELLLLLLLLLLLLLLHHHHHHHLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLL 1kct QELLRTLNQPDSQLQLTTGNGLFLSEGLKLVDKFLEDVKKLYHSEAFTVNFGDTEEAKKQINDYVEKGTQGKIVD        |   |  |       |    |    ||||  |      |  |    | |   | |   ||| |   | | | 1c5g RHLYKELMGPWNKDEISTTDAIFVQRDLKLVQGFMPHFFRLFRSTVKQVDFSEVERARFIINDWVKTHTKGMISN DSSP HHHHHHHLLHHHLLEEEEEEEEEEELLLLLLLLHHHHHHHHHLLLLEEELLLLHHHHHHHHHHHHHHHLLLLLLL DSSP LLL..LLLLLLLLLLLEELLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLLEELLLLLLLLLLL...LLLLLLLLLLLL 1kct LVK..ELDRDTVFALVNYIFFKGKWERPFEVKDTEEEDFHVDQVTTVKVPMMKRLGMFNIQHCKK...LSSWVLLMKYLG      |      |  |   |||   | | |  ||    |    ||     || ||||     ||              |   | | 1c5g LLGkgAVDQLTRLVLVNALYFNGQWKTPFPDSSTHRRLFHKSDGSTVSVPMMAQTNKFNYTEFTTpdgHYYDILELPYHG DSSP LLLhhHLLLLLLEEEEEEEEEEEELLLLLLLLLLEEEELLLLLLLLLEEEEEEEEEEEEEEEEEElllEEEEEEEEELLL DSSP .LEEEELLLLLL..LLLHHHLLLLLLHHHHHHHLLLLLLLLEEELLLLLLLLLLLLLLLHHHHLLHHHLLL 1kct .NATAIFFLPDE..GKLQHLENELTHDIITKFLENEDRRSASLHLPKLSITGTYDLKSVLGQLGITKVFSN               | |    |  | | |    |     |  |    | ||| |     ||   |  || |  | 1c5g dTLSMFIAAPYEkeVPLSALTNILSAQLISHWKGNMTRLPRLLVLPKFSLETEVDLRKPLENLGMTDMFRQ DSSP lLEEEEEEEELLllLLLHHHHLLLLHHHHHHHHLLLEEEEEEEEEELEEEEEEEELHHHHHHHLLLHHHLL DSSP L.LLLLLLLLLLLLLLLLLLLLLLLLLLLLllllllllllllllllllleelllLLLLLEEEELLLLLLLLEEELLLllll 1kct G.ADLSGVTEEAPLKLSKAVHKAVLTIDEKgteaagamfleaipmsippevkfnKPFVFLMIEQNTKSPLFMGKVVNptqk        ||        ||    |  |      |                          || |      |   |||| | 1c5g FqADFTSLSDQEPLHVAQALQKVKIEVNESgtvassstavivsarmapeeiimdRPFLFVVRHNPTGTVLFMGQVME...p DSSP LlLLLLLLLLLLLLLEEEEEEEEEEEELLLeeeeeeeeeeeellllllllllllLEEEEEEEELLLLEEEEEEEEEL...l *Z-score 31.9  AR 343  RMSD 2.9A  SI 30%

Structural alignment by DaliLite

[The DSSP code]

• H = alpha helix
• B = residue in isolated beta-bridge
• E = extended strand, participates in beta ladder
• G = 3-helix (3/10 helix)
• I = 5 helix (pi helix)
• T = hydrogen bonded turn
• S = bend
• L = no assigned structure

[The 5-tile code]

• 0 = DDDDD    (extended strand, small blue spheres)
• 1 = DDDDU
• 2 = DDDUD
• 3 = DDDUU
• 8 = DUDDD
• 9 = DUDDU
• A = DUDUD    (helix, large red spheres)
• B = DUDUU    (turn, large yellow spheres)
• G = UDDDD
• H = UDDDU
• I = UDDUD
• J = UDDUU
• O = UUDDD
• P = UUDDU
• Q = UUDUD    (turn, large yellow spheres)
• R = UUDUU    (turn, large yellow spheres)