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(-) Description

Title :  CRYSTAL STRUCTURE OF DE NOVO DESIGNED MID1-ZINC
 
Authors :  B. S. Der, M. Machius, M. J. Miley, B. Kuhlman
Date :  09 Dec 11  (Deposition) - 11 Jan 12  (Release) - 07 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.13
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Helix-Turn-Helix, Metal Binding, Homodimer, Metal Binding Protein, Hydrolase, De Novo Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. S. Der, M. Machius, M. J. Miley, J. L. Mills, T. Szyperski, B. Kuhlman
Metal-Mediated Affinity And Orientation Specificity In A Computationally Designed Protein Homodimer.
J. Am. Chem. Soc. V. 134 375 2012
PubMed-ID: 22092237  |  Reference-DOI: 10.1021/JA208015J

(-) Compounds

Molecule 1 - COMPUTATIONAL DESIGN, MID1-ZINC
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PQE-80L MBP FUSION
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Organism Scientific: ARTIFICIAL GENE
    Organism Taxid: 32630
    Synonym: COMPUTATIONAL REDESIGN OF THE BIOLOGICAL SEQUENCE.

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric/Biological Unit (3, 4)
No.NameCountTypeFull Name
1TLA1Ligand/IonL(+)-TARTARIC ACID
2UNL1Ligand/IonUNKNOWN LIGAND
3ZN2Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:12 , HIS A:16 , TLA A:102 , HIS B:39BINDING SITE FOR RESIDUE ZN A 101
2AC2SOFTWAREHIS A:12 , HIS A:16 , LYS A:19 , ARG A:23 , GLN A:31 , HIS A:35 , ZN A:101 , HOH A:228 , HOH A:237 , HIS B:35 , HIS B:39BINDING SITE FOR RESIDUE TLA A 102
3AC3SOFTWAREHIS A:39 , HIS B:12 , HIS B:16 , ASP B:46BINDING SITE FOR RESIDUE ZN B 101

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V1C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V1C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V1C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V1C)

(-) Exons   (0, 0)

(no "Exon" information available for 3V1C)

(-) Sequences/Alignments

Asymmetric/Biological 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:46
                                                                             
               SCOP domains ---------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------- PROSITE
                 Transcript ---------------------------------------------- Transcript
                  3v1c A  1 GSPLAQQIKNIHSFIHQAKAAGRMDEVRTLQENLHQLMHEYFQQSD 46
                                    10        20        30        40      


Chain B from PDB  Type:PROTEIN  Length:47
                                                                              
               SCOP domains ----------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------- PROSITE
                 Transcript ----------------------------------------------- Transcript
                  3v1c B  0 SGSPLAQQIKNIHSFIHQAKAAGRMDEVRTLQENLHQLMHEYFQQSD 46
                                     9        19        29        39
   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  (0, 0)

(no "SCOP Domain" information available for 3V1C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V1C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V1C)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3V1C)

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  3v1c
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

(no "Entries Sharing at Least One Protein Chain" available for 3V1C)

(-) Related Entries Specified in the PDB File

1yzm THIS DEPOSITION IS A COMPUTATIONAL REDESIGN OF 1YZM.
3v1a
3v1b
3v1d
3v1e
3v1f