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(-) Description

Title :  CRYSTAL STRUCTURE OF PHD TRUNCATED TO RESIDUE 57 IN AN ORTHORHOMBIC SPACE GROUP
 
Authors :  A. Garcia-Pino, R. Loris
Date :  10 Jun 09  (Deposition) - 23 Jun 10  (Release) - 21 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,G  (1x)
Biol. Unit 2:  B,C,D  (1x)
Biol. Unit 3:  D,E,F  (1x)
Biol. Unit 4:  F,G,H  (1x)
Keywords :  Prevent Host Death, Phd, Intrinsic Disorder, Doc, Toxin-Antitoxin, Antitoxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Garcia-Pino, S. Balasubramanian, L. Wyns, E. Gazit, H. De Greve, R. D. Magnuson, D. Charlier, N. A. Van Nuland, R. Loris
Allostery And Intrinsic Disorder Mediate Transcription Regulation By Conditional Cooperativity.
Cell(Cambridge, Mass. ) V. 142 101 2010
PubMed-ID: 20603017  |  Reference-DOI: 10.1016/J.CELL.2010.05.039

(-) Compounds

Molecule 1 - PREVENT HOST DEATH PROTEIN
    Chains: A, B, C, D, E, F, G, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET21B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PHD
    Organism Common: BACTERIOPHAGE P1
    Organism Scientific: ENTEROBACTERIA PHAGE P1
    Organism Taxid: 10678
    Synonym: PHD PROTEIN

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB    G 
Biological Unit 2 (1x):  BCD    
Biological Unit 3 (1x):    DEF  
Biological Unit 4 (1x):      FGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1SO46Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
Biological Unit 4 (1, 3)
No.NameCountTypeFull Name
1SO43Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN B:12 , ASN B:19BINDING SITE FOR RESIDUE SO4 B 106
2AC2SOFTWAREASN C:5 , PHE C:6 , ARG C:7 , THR C:29 , ARG C:30 , ARG C:31BINDING SITE FOR RESIDUE SO4 C 102
3AC3SOFTWAREASN D:5 , PHE D:6 , ARG D:7 , THR D:29 , ARG D:30 , ARG D:31BINDING SITE FOR RESIDUE SO4 D 101
4AC4SOFTWAREASN F:5 , PHE F:6 , ARG F:7 , THR F:29BINDING SITE FOR RESIDUE SO4 F 103
5AC5SOFTWAREASN G:5 , PHE G:6 , ARG G:7 , THR G:29 , ARG G:31BINDING SITE FOR RESIDUE SO4 G 105
6AC6SOFTWAREASN H:12BINDING SITE FOR RESIDUE SO4 H 107

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3HS2)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Glu C:55 -Phe C:56

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3HS2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3HS2)

(-) Exons   (0, 0)

(no "Exon" information available for 3HS2)

(-) 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:56
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:56
                                    10        20        30        40        50      
              PHD_BPP1    1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEF 56
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhh...eeee......eeeeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  3hs2 A  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEF 56
                                    10        20        30        40        50      


Chain B from PDB  Type:PROTEIN  Length:56
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:56
                                    10        20        30        40        50      
              PHD_BPP1    1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEF 56
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhh...eeeee..eeeeeeeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  3hs2 B  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEF 56
                                    10        20        30        40        50      


Chain C from PDB  Type:PROTEIN  Length:58
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:58
                                    10        20        30        40        50        
              PHD_BPP1    1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEFAS 58
               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
                  3hs2 C  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEFAS 58
                                    10        20        30        40        50        


Chain D from PDB  Type:PROTEIN  Length:56
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:56
                                    10        20        30        40        50      
              PHD_BPP1    1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEF 56
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhh...eeee......eeeeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  3hs2 D  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEF 56
                                    10        20        30        40        50      


Chain E from PDB  Type:PROTEIN  Length:54
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:54
                                    10        20        30        40        50    
              PHD_BPP1    1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDA 54
               SCOP domains ------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhh...eeee......eeeeehhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------ Transcript
                  3hs2 E  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDA 54
                                    10        20        30        40        50    


Chain F from PDB  Type:PROTEIN  Length:55
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:55
                                    11        21        31        41        51     
              PHD_BPP1    2 QSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEF 56
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .eeehhhhhhhhhhhhhhhhh...eeee......eeeeehhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  3hs2 F  2 QSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAEF 56
                                    11        21        31        41        51     


Chain G from PDB  Type:PROTEIN  Length:52
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:52
                                    10        20        30        40        50  
              PHD_BPP1    1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAAL 52
               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
                  3hs2 G  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAAL 52
                                    10        20        30        40        50  


Chain H from PDB  Type:PROTEIN  Length:55
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:55
                                    10        20        30        40        50     
              PHD_BPP1    1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAE 55
               SCOP domains ------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeehhhhhhhhhhhhhhhhh...eeee......eeeeehhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------- Transcript
                  3hs2 H  1 MQSINFRTARGNLSEVLNNVEAGEEVEITRRGREPAVIVSKATFEAYKKAALDAE 55
                                    10        20        30        40        50
   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 3HS2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3HS2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3HS2)

(-) Gene Ontology  (3, 3)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (PHD_BPP1 | Q06253)
molecular function
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PHD_BPP1 | Q06253: 3dd7 3hry 3k33 3kh2 4zlx 4zm0 4zm2

(-) Related Entries Specified in the PDB File

3dd7 CRYSTAL STRUCTURE OF C-TERMINAL DOMAIN OF PHD
3hry CRYSTAL STRUCTURE OF FULL LENGTH PHD FROM BACTERIOPHAGE P1