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(-) Description

Title :  ANTITOXIN PHD FROM PHAGE P1 IN COMPLEX WITH ITS OPERATOR DNA INVERTED REPEAT IN A MONOCLINIC SPACE GROUP
 
Authors :  A. Garcia-Pino, R. Loris
Date :  02 May 15  (Deposition) - 20 Apr 16  (Release) - 29 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.88
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,G,H  (1x)
Biol. Unit 2:  C,D,E,F  (1x)
Keywords :  Transcription Factor, Toxin-Antitoxin, Dna Binding, Intrinsic Disorder, Conditional Cooperativity, Protein-Dna Complex, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Garcia-Pino, S. De Gieter, A. Talavera, H. De Greve, R. G. Efremov R. Loris
An Intrinsically Disordered Entropic Switch Determines Allostery In Phd-Doc Regulation.
Nat. Chem. Biol. V. 12 490 2016
PubMed-ID: 27159580  |  Reference-DOI: 10.1038/NCHEMBIO.2078

(-) Compounds

Molecule 1 - ANTITOXIN PHD
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Taxid: 469008
    Gene: PHD
    Organism Scientific: ENTEROBACTERIA PHAGE P1
    Organism Taxid: 10678
    Synonym: ADDICTION PROTEIN PDH,PREVENT HOST DEATH PROTEIN
 
Molecule 2 - DNA (5'-D(GP*CP*TP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*T)-3')
    Chains: E, G
    Engineered: YES
    Organism Scientific: ENTEROBACTERIA PHAGE P1
    Organism Taxid: 10678
    Synthetic: YES
 
Molecule 3 - DNA (5'-D(CP*AP*TP*GP*TP*GP*TP*AP*CP*AP*CP*AP*AP*G)-3')
    Chains: F, H
    Engineered: YES
    Organism Scientific: ENTEROBACTERIA PHAGE P1
    Organism Taxid: 10678
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB    GH
Biological Unit 2 (1x):   CDEF  

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4ZM2)

(-) Sites  (0, 0)

(no "Site" information available for 4ZM2)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4ZM2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Leu B:59 -Phe B:60

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4ZM2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4ZM2)

(-) Exons   (0, 0)

(no "Exon" information available for 4ZM2)

(-) 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:52
                                                                                   
               SCOP domains ---------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhh...eeeee..eeeeeeeehhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------- Transcript
                  4zm2 A  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAAL 52
                                    10        20        30        40        50  


Chain B from PDB  Type:PROTEIN  Length:61
                                                                                            
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhh...eeee......eeeeehhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                  4zm2 B  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEFASLFD 61
                                    10        20        30        40        50        60 


Chain C from PDB  Type:PROTEIN  Length:55
                                                                                      
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhh...eeee......eeeeehhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  4zm2 C  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAE 55
                                    10        20        30        40        50     


Chain D from PDB  Type:PROTEIN  Length:53
                                                                                    
               SCOP domains ----------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhh...eeee......eeeeehhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------- Transcript
                  4zm2 D  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALD 53
                                    10        20        30        40        50   


Chain E from PDB  Type:DNA  Length:14
                                             
                  4zm2 E  1 GCTTGTGTACACAT 14
                                    10    


Chain F from PDB  Type:DNA  Length:14
                                             
                  4zm2 F  1 CATGTGTACACAAG 14
                                    10    


Chain G from PDB  Type:DNA  Length:14
                                             
                  4zm2 G  1 GCTTGTGTACACAT 14
                                    10    


Chain H from PDB  Type:DNA  Length:13
                                            
                  4zm2 H  2 ATGTGTACACAAG 14
                                    11
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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 4ZM2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4ZM2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4ZM2)

(-) Gene Ontology  (3, 3)

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  Cis Peptide Bonds
    Leu B:59 - Phe B:60   [ RasMol ]  
 
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 Related Entries

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        PHD_BPP1 | Q06253: 3dd7 3hry 3hs2 3k33 3kh2 4zlx 4zm0

(-) Related Entries Specified in the PDB File

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