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(-) Description

Title :  COMPUTER-BASED REDESIGN OF A BETA SANDWICH PROTEIN SUGGESTS THAT EXTENSIVE NEGATIVE DESIGN IS NOT REQUIRED FOR DE NOVO BETA SHEET DESIGN.
 
Authors :  X. Hu, H. Ke, B. Kuhlman
Date :  31 Oct 07  (Deposition) - 04 Nov 08  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A (4x),B (4x),C (4x),D (4x),E (4x),F (4x),G (4x),H (4x)
Biol. Unit 2:  A,E  (1x)
Biol. Unit 3:  B,G  (1x)
Biol. Unit 4:  C,F  (1x)
Biol. Unit 5:  D,H  (1x)
Keywords :  Beta Sheet, Computational Redesigned Protein, Cell Adhesion, Egf-Like Domain, Extracellular Matrix, Glycoprotein, Phosphorylation, Secreted, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Hu, H. Wang, H. Ke, B. Kuhlman
Computer-Based Redesign Of A Beta Sandwich Protein Suggests That Extensive Negative Design Is Not Required For De Novo Beta Sheet Design.
Structure V. 16 1799 2008
PubMed-ID: 19081056  |  Reference-DOI: 10.1016/J.STR.2008.09.013

(-) Compounds

Molecule 1 - TEN-D3
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (4x): A (4x)B (4x)C (4x)D (4x)E (4x)F (4x)G (4x)H (4x)
Biological Unit 2 (1x): A   E   
Biological Unit 3 (1x):  B    G 
Biological Unit 4 (1x):   C  F  
Biological Unit 5 (1x):    D   H

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3B83)

(-) Sites  (0, 0)

(no "Site" information available for 3B83)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3B83)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3B83)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3B83)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3B83)

(-) Exons   (0, 0)

(no "Exon" information available for 3B83)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:95
                                                                                                                              
               SCOP domains d3b83a_ A: automated matches                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee......eeeeee.......eeeeeeee.......eeeee...eeeeee.......eeeeeeeeee..ee...eeeeee...... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                  3b83 A  0 MLQPPFNIKVTNITLTTAVVTWQPPILPIEGILVTFGRKNDPSDETTVDLTSSITSLTLTNLEPNTTYEIRIVARNGQQYSPPVSTTFTTGSLEH 94
                                     9        19        29        39        49        59        69        79        89     


Chain B from PDB  Type:PROTEIN  Length:92
                                                                                                                           
               SCOP domains d3b83b_ B: automated matches                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee......eeeeee.......eeeeeeee.......eeeee...eeeeee.......eeeeeeeeee..ee...eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  3b83 B  1 LQPPFNIKVTNITLTTAVVTWQPPILPIEGILVTFGRKNDPSDETTVDLTSSITSLTLTNLEPNTTYEIRIVARNGQQYSPPVSTTFTTGSL 92
                                    10        20        30        40        50        60        70        80        90  


Chain C from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains d3b83c_ C: automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee......eeeeee.......eeeeeeee.......eeeee...eeeeee.......eeeeeeeeee..ee...eeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  3b83 C  0 MLQPPFNIKVTNITLTTAVVTWQPPILPIEGILVTFGRKNDPSDETTVDLTSSITSLTLTNLEPNTTYEIRIVARNGQQYSPPVSTTFTTGSLEHHHHH 98
                                     9        19        29        39        49        59        69        79        89         


Chain D from PDB  Type:PROTEIN  Length:91
                                                                                                                          
               SCOP domains d3b83d_ D: automated matches                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee......eeeeee.......eeeeeeee.......eeeee...eeeeee.......eeeeeeeeee..ee...eeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------- Transcript
                  3b83 D  1 LQPPFNIKVTNITLTTAVVTWQPPILPIEGILVTFGRKNDPSDETTVDLTSSITSLTLTNLEPNTTYEIRIVARNGQQYSPPVSTTFTTGS 91
                                    10        20        30        40        50        60        70        80        90 


Chain E from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains d3b83e_ E: automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee......eeeeee.......eeeeeeee.......eeeee...eeeeee.......eeeeeeeeee..ee...eeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  3b83 E  0 MLQPPFNIKVTNITLTTAVVTWQPPILPIEGILVTFGRKNDPSDETTVDLTSSITSLTLTNLEPNTTYEIRIVARNGQQYSPPVSTTFTTGSLEHHHHH 98
                                     9        19        29        39        49        59        69        79        89         


Chain F from PDB  Type:PROTEIN  Length:92
                                                                                                                           
               SCOP domains d3b83f_ F: automated matches                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee......eeeeee........eeeeeee.......eeeee...eeeeee.......eeeeeeee.........eeeeee.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                  3b83 F  1 LQPPFNIKVTNITLTTAVVTWQPPILPIEGILVTFGRKNDPSDETTVDLTSSITSLTLTNLEPNTTYEIRIVARNGQQYSPPVSTTFTTGSL 92
                                    10        20        30        40        50        60        70        80        90  


Chain G from PDB  Type:PROTEIN  Length:99
                                                                                                                                  
               SCOP domains d3b83g_ G: automated matches                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee......eeeeee.......eeeeeeee.......eeeee...eeeeee.......eeeeeeeeee..ee...eeeeee.......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                  3b83 G  0 MLQPPFNIKVTNITLTTAVVTWQPPILPIEGILVTFGRKNDPSDETTVDLTSSITSLTLTNLEPNTTYEIRIVARNGQQYSPPVSTTFTTGSLEHHHHH 98
                                     9        19        29        39        49        59        69        79        89         


Chain H from PDB  Type:PROTEIN  Length:94
                                                                                                                             
               SCOP domains d3b83h_ H: automated matches                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee......eeeeee.......eeeeeeee.......eeeee...eeeeee.......eeeeeeeee........eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------- Transcript
                  3b83 H  0 MLQPPFNIKVTNITLTTAVVTWQPPILPIEGILVTFGRKNDPSDETTVDLTSSITSLTLTNLEPNTTYEIRIVARNGQQYSPPVSTTFTTGSLE 93
                                     9        19        29        39        49        59        69        79        89
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 8)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3B83)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3B83)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3B83)

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  3b83
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