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(-) Description

Title :  DESIGN OF A BINDING SCAFFOLD BASED ON VARIABLE LYMPHOCYTE RECEPTORS OF JAWLESS VERTEBRATES BY MODULE ENGINEERING
 
Authors :  H. J. Kim, H. K. Cheong, Y. H. Jeon
Date :  06 Apr 11  (Deposition) - 14 Mar 12  (Release) - 14 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.78
Chains :  Asym./Biol. Unit :  A
Keywords :  Lrr, Protein Binding, Plasma (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. C. Lee, K. Park, J. Han, J. J. Lee, H. J. Kim, S. Hong, W. Heu, Y. J. Kim, J. S. Ha, S. G. Lee, H. K. Cheong, Y. H. Jeon, D. Kim, H. S. Kim
Design Of A Binding Scaffold Based On Variable Lymphocyte Receptors Of Jawless Vertebrates By Module Engineering
Proc. Natl. Acad. Sci. Usa V. 109 3299 2012
PubMed-ID: 22328160  |  Reference-DOI: 10.1073/PNAS.1113193109

(-) Compounds

Molecule 1 - INTERNALIN B, REPEAT MODULES, VARIABLE LYMPHOCYTE RECEPTOR
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: MARINE LAMPREY
    Organism Scientific: LISTERIA MONOCYTOGENES, SYNTHETIC, PETROMYZON MARINUS
    Organism Taxid: 637381, 32630, 7757
    Other Details: CHIMERA OF INTERNALIN B, REPEAT MODULES, VARIABLE LYMPHOCYTE RECEPTOR
    Strain: 08-5923

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:36 , ASN A:38 , GLU A:39 , ASP A:52 , LYS A:54 , LYS A:74BINDING SITE FOR RESIDUE SO4 A 280
2AC2SOFTWARETYR A:137 , THR A:160 , ARG A:161 , LYS A:184 , ARG A:250BINDING SITE FOR RESIDUE SO4 A 281

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:219 -A:251
2A:221 -A:271

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3RFJ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3RFJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3RFJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3RFJ)

(-) Sequences/Alignments

Asymmetric/Biological Unit
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Chain A from PDB  Type:PROTEIN  Length:268
 aligned with Q6E4K6_PETMA | Q6E4K6 from UniProtKB/TrEMBL  Length:270

    Alignment length:268
                                                                                                   40                                               48                                                                                                                                                  
                               1          13             14                     37               38 |                    41   46                   47|      49                                                                                                                                          
                               |     7     |   -         -|       23        33   |     -         -| |      -         -    |   46         -         -||      49        59        69        79        89        99       109       119       129       139       149       159       169       179        
         Q6E4K6_PETMA     - ---MWIKWIATLVAFG--------------ALVQSAVACPSQCSCSGTTVDCRS----------------KRH---------------------ASVPAG--------------------IP-------TNAQILYLHDNQITKLEPGVFDHLVNLQGLGLQNNQLTSLPNGVFNKLTQLTHLSLYNNQLKSIPRGAFDNLKSLTQIWLYNNPWDCACSDILYLSRWISQHPGLVFGYLNLDPDSARCSGTNTPVRAVTEASTSPSKC 187
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eehhhhh.hhhhhhhhhhhh.......eehhhhhhh..eee..........hhhhh....eee........hhhhh......eee.....................eee.....................eee.....................eee.....................eee.....................eee.........hhhhhhhhhhhhhh...ee.................hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3rfj A   4 TVSTPIKQIFPDDAFAETIKANLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVRYLALGGNKLHDISALKELTNLTYLILTGNQLQSLPNGVFDKLTNLKELVLVENQLQSLPDGVFDKLTNLTYLYLYHNQLQSLPKGVFDKLTNLTRLDLDNNQLQSLPEGVFDKLTQLKQLSLNDNQLKSVPDGVFDRLTSLTHIWLLNNPWDCACSDILYLSRWISQHPGLVFGYLNLDPDSARCSGTNTPVRAVTEASTSPSKC 271
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3RFJ)

(-) CATH Domains  (0, 0)

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(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
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3rfs