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(-) Description

Title :  COMPUTATIONALLY DESIGNED LEFT-HANDED ALPHA/ALPHA TOROID WITH 3 REPEATS IN SPACE GROUP P212121
 
Authors :  J. P. Hallinan, P. Bradley, B. L. Stoddard
Date :  23 Mar 15  (Deposition) - 16 Dec 15  (Release) - 06 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
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 :  Rosetta, Toroid, Alpha Helix, Computationally Designed, Left-Handed, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Doyle, J. Hallinan, J. Bolduc, F. Parmeggiani, D. Baker, B. L. Stoddard, P. Bradley
Rational Design Of Alpha-Helical Tandem Repeat Proteins Wit Closed Architectures.
Nature V. 528 585 2015
PubMed-ID: 26675735  |  Reference-DOI: 10.1038/NATURE16191

(-) Compounds

Molecule 1 - DTOR_3X33L
    Chains: A, B, C, D
    Engineered: YES
    Fragment: DTOR_3X33L
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Other Details: ROSETTA DESIGNED
    Synthetic: YES

 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  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1NA8Ligand/IonSODIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 3 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION
Biological Unit 4 (0, 0)
No.NameCountTypeFull Name
1NA-1Ligand/IonSODIUM ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:332binding site for residue NA A 201
2AC2SOFTWAREGLU A:23 , HOH A:312 , HOH A:335binding site for residue NA A 202
3AC3SOFTWAREHOH A:336 , THR B:72 , HOH B:308binding site for residue NA B 201
4AC4SOFTWAREHOH A:337 , SER B:70 , HOH B:335binding site for residue NA B 202
5AC5SOFTWARETHR B:20 , HOH B:330 , HOH D:225binding site for residue NA B 203
6AC6SOFTWAREHOH B:337 , HOH B:339 , HOH B:340binding site for residue NA B 204
7AC7SOFTWAREHOH B:322 , HOH B:346 , HOH D:221binding site for residue NA B 205
8AC8SOFTWAREHOH B:333 , HOH B:340binding site for residue NA B 206

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YY2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YY2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YY2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YY2)

(-) Exons   (0, 0)

(no "Exon" information available for 4YY2)

(-) 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:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4yy2 A   2 GKSPTEVLLELIAEASGTTREEVKEKFLKELRKGKSPTEVLLELIAEASGTTKEEVKEKFLKELSFGKSPTEVLLELIAEASGTTKEEVKKKFWKELSL 100
                                    11        21        31        41        51        61        71        81        91         


Chain B from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4yy2 B   2 GKSPTEVLLELIAEASGTTREEVKEKFLKELRKGKSPTEVLLELIAEASGTTKEEVKEKFLKELSFGKSPTEVLLELIAEASGTTKEEVKKKFWKELSL 100
                                    11        21        31        41        51        61        71        81        91         


Chain C from PDB  Type:PROTEIN  Length:98
                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------- Transcript
                 4yy2 C   3 KSPTEVLLELIAEASGTTREEVKEKFLKELRKGKSPTEVLLELIAEASGTTKEEVKEKFLKELSFGKSPTEVLLELIAEASGTTKEEVKKKFWKELSL 100
                                    12        22        32        42        52        62        72        82        92        


Chain D from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4yy2 D   2 GKSPTEVLLELIAEASGTTREEVKEKFLKELRKGKSPTEVLLELIAEASGTTKEEVKEKFLKELSFGKSPTEVLLELIAEASGTTKEEVKKKFWKELSL 100
                                    11        21        31        41        51        61        71        81        91
   Legend:   → Mismatch (orange background)
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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 4YY2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YY2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YY2)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4YY2)

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  4yy2
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