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(-) Description

Title :  CRYSTAL STRUCTURE OF SYMFOIL-2: DE NOVO DESIGNED BETA-TREFOIL ARCHITECTURE WITH SYMMETRIC PRIMARY STRUCTURE
 
Authors :  J. Lee, M. Blaber
Date :  26 Jul 10  (Deposition) - 22 Dec 10  (Release) - 22 Jun 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Beta-Trefoil, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Lee, M. Blaber
Experimental Support For The Evolution Of Symmetric Protein Architecture From A Simple Peptide Motif.
Proc. Natl. Acad. Sci. Usa V. 108 126 2011
PubMed-ID: 21173271  |  Reference-DOI: 10.1073/PNAS.1015032108

(-) Compounds

Molecule 1 - DE NOVO DESIGNED BETA-TREFOIL ARCHITECTURE WITH SYMMETRIC PRIMARY STRUCTURE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: ARTIFICIAL GENE
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric Unit (2, 14)
No.NameCountTypeFull Name
1SO410Ligand/IonSULFATE ION
2TRS4Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 3 (2, 4)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Biological Unit 4 (2, 3)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2TRS1Ligand/Ion2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETHR A:30 , VAL A:31 , THR A:72 , VAL A:73 , THR A:116 , VAL A:117 , HOH A:152 , HOH A:153 , HOH A:163BINDING SITE FOR RESIDUE TRS A 141
02AC2SOFTWAREARG A:66 , THR A:76 , HOH A:288 , HOH A:421 , HOH A:578BINDING SITE FOR RESIDUE SO4 A 142
03AC3SOFTWAREARG A:35 , HOH A:173 , SER C:38 , LYS D:15 , GLY D:20 , HOH D:359 , HOH D:410 , HOH D:546 , HOH D:597BINDING SITE FOR RESIDUE SO4 A 143
04AC4SOFTWARETHR B:30 , VAL B:31 , THR B:72 , VAL B:73 , THR B:116 , VAL B:117 , HOH B:163 , HOH B:167BINDING SITE FOR RESIDUE TRS B 141
05AC5SOFTWAREASP B:39 , GLN B:40 , HOH B:189 , HOH B:394 , HOH B:529 , ARG D:24BINDING SITE FOR RESIDUE SO4 B 142
06AC6SOFTWAREARG B:66 , THR B:76 , HOH B:190BINDING SITE FOR RESIDUE SO4 B 143
07AC7SOFTWAREARG B:35 , HOH B:174 , HOH B:378 , LYS C:15 , GLY C:20 , HOH C:284 , SER D:38 , HOH D:333BINDING SITE FOR RESIDUE SO4 B 144
08AC8SOFTWARETHR C:30 , VAL C:31 , THR C:72 , VAL C:73 , THR C:116 , VAL C:117 , HOH C:154 , HOH C:155 , HOH C:157BINDING SITE FOR RESIDUE TRS C 141
09AC9SOFTWARESER A:38 , GLN A:40 , HOH A:167 , ARG C:24 , HOH C:226 , HOH C:540BINDING SITE FOR RESIDUE SO4 C 142
10BC1SOFTWAREARG C:66 , THR C:76 , HOH C:156 , HOH C:348 , HOH C:497BINDING SITE FOR RESIDUE SO4 C 143
11BC2SOFTWAREARG A:110 , THR A:123 , HOH A:157 , ARG C:110 , THR C:123 , HOH C:184 , HOH C:237 , HOH C:526 , HOH C:622BINDING SITE FOR RESIDUE SO4 C 144
12BC3SOFTWARETHR D:30 , VAL D:31 , THR D:72 , VAL D:73 , THR D:116 , VAL D:117 , HOH D:155 , HOH D:156BINDING SITE FOR RESIDUE TRS D 141
13BC4SOFTWAREARG D:66 , THR D:76 , HOH D:341 , HOH D:342BINDING SITE FOR RESIDUE SO4 D 142
14BC5SOFTWAREARG B:110 , THR B:123 , HOH B:183 , HOH B:196 , ARG D:110 , THR D:123 , HOH D:212 , HOH D:536 , HOH D:604 , HOH D:628BINDING SITE FOR RESIDUE SO4 D 143

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3O4A)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3O4A)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3O4A)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3O4A)

(-) Exons   (0, 0)

(no "Exon" information available for 3O4A)

(-) 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:123
                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeee.....eeee.........eeeeee...eeeeee.....eeee.....eeee.........eeeee....eeeeee....eeeee.....eeee.........eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                3o4a A   11 PVLLKSTETGQYLRINPDGTVDGTRDRSDQHIQFQISPEGGGEVLLKSTETGQYLRINPDGTVDGTRDRSDQHIQFQISPEGGGEVLLKSTETGQYLRINPDGTVDGTRDRSDQHIQFQISPE  137
                                    20        30        40        50        60        70      | 79        89        99   ||  112      |124       134   
                                                                                            76A                        103|         119||              
                                                                                                                        107          123|              
                                                                                                                                     123A              


Chain B from PDB  Type:PROTEIN  Length:123
                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeee.....eeee.........eeeeee...eeeeee.....eeee.....eeee.........eeeee.....eeeee....eeeee.....eeee.........eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                3o4a B   11 PVLLKSTETGQYLRINPDGTVDGTRDRSDQHIQFQISPEGGGEVLLKSTETGQYLRINPDGTVDGTRDRSDQHIQFQISPEGGGEVLLKSTETGQYLRINPDGTVDGTRDRSDQHIQFQISPE  137
                                    20        30        40        50        60        70      | 79        89        99   ||  112      |124       134   
                                                                                            76A                        103|         119||              
                                                                                                                        107          123|              
                                                                                                                                     123A              


Chain C from PDB  Type:PROTEIN  Length:123
                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeee.....eeee....hhhh.eeeeee...eeeeee.....eeee.....eeee.........eeeee.....eeeee.....eeee.....eeee.........eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                3o4a C   11 PVLLKSTETGQYLRINPDGTVDGTRDRSDQHIQFQISPEGGGEVLLKSTETGQYLRINPDGTVDGTRDRSDQHIQFQISPEGGGEVLLKSTETGQYLRINPDGTVDGTRDRSDQHIQFQISPE  137
                                    20        30        40        50        60        70      | 79        89        99   ||  112      |124       134   
                                                                                            76A                        103|         119||              
                                                                                                                        107          123|              
                                                                                                                                     123A              


Chain D from PDB  Type:PROTEIN  Length:123
                                                                                                                                                            
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.....eeee.....eeee....hhhh.eeeeee...eeeeee.....eeee.....eeee.........eeeee.....eeeee.....eeee.....eeee.........eeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                3o4a D   11 PVLLKSTETGQYLRINPDGTVDGTRDRSDQHIQFQISPEGGGEVLLKSTETGQYLRINPDGTVDGTRDRSDQHIQFQISPEGGGEVLLKSTETGQYLRINPDGTVDGTRDRSDQHIQFQISPE  137
                                    20        30        40        50        60        70      | 79        89        99   ||  112      |124       134   
                                                                                            76A                        103|         119||              
                                                                                                                        107          123|              
                                                                                                                                     123A
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  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  (0, 0)

(no "SCOP Domain" information available for 3O4A)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3O4A)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3O4A)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
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 Related Entries

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(-) Related Entries Specified in the PDB File

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3o4d
3o4e