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(-) Description

Title :  CRYSTAL STRUCTURE OF DE NOVO DESIGNED MID1-COBALT
 
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 :  1.24
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,F  (1x)
Biol. Unit 2:  B,C  (1x)
Biol. Unit 3:  D,G  (1x)
Biol. Unit 4:  E,H  (1x)
Keywords :  Helix-Turn-Helix, Zinc Homodimerization, De Novo Protein, Metal Binding 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-COBALT
    Chains: A, B, C, D, E, F, G, H
    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

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 12)

Asymmetric Unit (2, 12)
No.NameCountTypeFull Name
11PE4Ligand/IonPENTAETHYLENE GLYCOL
2CO8Ligand/IonCOBALT (II) ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CO-1Ligand/IonCOBALT (II) ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CO-1Ligand/IonCOBALT (II) ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CO-1Ligand/IonCOBALT (II) ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
2CO-1Ligand/IonCOBALT (II) ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHIS A:35 , HIS A:39 , ASP A:46 , HIS F:12 , HIS F:16BINDING SITE FOR RESIDUE CO A 47
02AC2SOFTWAREILE A:15 , HIS A:16 , HIS A:35 , HOH A:426 , ILE F:15 , HIS F:16 , HIS F:35 , HOH F:159 , HOH F:473BINDING SITE FOR RESIDUE 1PE A 48
03AC3SOFTWAREHIS B:35 , HIS B:39 , HIS C:12 , HIS C:16 , ASP C:46BINDING SITE FOR RESIDUE CO B 47
04AC4SOFTWAREHIS B:12 , HIS B:16 , HIS C:35 , HIS C:39 , ASP C:46BINDING SITE FOR RESIDUE CO C 47
05AC5SOFTWAREILE B:15 , HIS B:16 , LEU B:34 , HIS B:35 , ILE C:15 , HIS C:16 , HIS C:35 , HOH C:416 , HOH C:417 , HOH C:435BINDING SITE FOR RESIDUE 1PE C 48
06AC6SOFTWAREHIS E:35 , HIS E:39 , HIS H:12 , HIS H:16 , ASP H:46BINDING SITE FOR RESIDUE CO E 47
07AC7SOFTWAREILE E:15 , HIS E:16 , LYS E:19 , LEU E:34 , HIS E:35 , HOH E:121 , HOH E:168 , HOH E:429 , ILE H:15 , HIS H:16 , LYS H:19 , HIS H:35BINDING SITE FOR RESIDUE 1PE E 48
08AC8SOFTWAREHIS A:12 , HIS A:16 , ASP A:46 , HIS F:35 , HIS F:39BINDING SITE FOR RESIDUE CO F 47
09AC9SOFTWAREHIS D:35 , HIS D:39 , ASP D:46 , HIS G:12 , HIS G:16BINDING SITE FOR RESIDUE CO G 47
10BC1SOFTWAREHIS D:12 , HIS D:16 , ASP D:46 , HIS G:35 , HIS G:39BINDING SITE FOR RESIDUE CO G 48
11BC2SOFTWAREILE D:15 , HIS D:16 , LYS D:19 , HIS D:35 , ILE G:15 , HIS G:16 , LYS G:19 , LEU G:34 , HIS G:35 , HOH G:160 , HOH G:423BINDING SITE FOR RESIDUE 1PE G 49
12BC3SOFTWAREHIS E:12 , HIS E:16 , HIS H:35 , HIS H:39 , ASP H:46BINDING SITE FOR RESIDUE CO H 47

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3V1D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3V1D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3V1D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3V1D)

(-) Exons   (0, 0)

(no "Exon" information available for 3V1D)

(-) 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:48
                                                                               
               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
                  3v1d A -1 GSGSPLAQQIKNIHSFIHQAKAAGRMDEVRTLQENLHQLMHEYFQQSD 46
                                     8        18        28        38        


Chain B from PDB  Type:PROTEIN  Length:48
                                                                               
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                  3v1d B -1 GSGSPLAQQIKNIHSFIHQAKAAGRMDEVRTLQENLHQLMHEYFQQSD 46
                                     8        18        28        38        


Chain C from PDB  Type:PROTEIN  Length:48
                                                                               
               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
                  3v1d C -1 GSGSPLAQQIKNIHSFIHQAKAAGRMDEVRTLQENLHQLMHEYFQQSD 46
                                     8        18        28        38        


Chain D from PDB  Type:PROTEIN  Length:48
                                                                               
               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
                  3v1d D -1 GSGSPLAQQIKNIHSFIHQAKAAGRMDEVRTLQENLHQLMHEYFQQSD 46
                                     8        18        28        38        


Chain E from PDB  Type:PROTEIN  Length:48
                                                                               
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                  3v1d E -1 GSGSPLAQQIKNIHSFIHQAKAAGRMDEVRTLQENLHQLMHEYFQQSD 46
                                     8        18        28        38        


Chain F from PDB  Type:PROTEIN  Length:48
                                                                               
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                  3v1d F -1 GSGSPLAQQIKNIHSFIHQAKAAGRMDEVRTLQENLHQLMHEYFQQSD 46
                                     8        18        28        38        


Chain G from PDB  Type:PROTEIN  Length:48
                                                                               
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                  3v1d G -1 GSGSPLAQQIKNIHSFIHQAKAAGRMDEVRTLQENLHQLMHEYFQQSD 46
                                     8        18        28        38        


Chain H from PDB  Type:PROTEIN  Length:48
                                                                               
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                  3v1d H -1 GSGSPLAQQIKNIHSFIHQAKAAGRMDEVRTLQENLHQLMHEYFQQSD 46
                                     8        18        28        38
   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 3V1D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3V1D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3V1D)

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3V1D)

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 Related Entries

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(-) Related Entries Specified in the PDB File

1yzm THIS DEPOSITION IS A COMPUTATIONAL REDESIGN OF 1YZM.
3v1a
3v1b
3v1c
3v1e
3v1f