Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF DOCH66Y IN COMPLEX WITH THE C-TERMINAL DOMAIN OF PHD
 
Authors :  A. Garcia-Pino, R. Loris
Date :  05 Jun 08  (Deposition) - 16 Sep 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  All Alpha, Ribosome Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Garcia-Pino, M. Christensen-Dalsgaard, L. Wyns, M. Yarmolinsky, R. D. Magnuson, K. Gerdes, R. Loris
Doc Of Prophage P1 Is Inhibited By Its Antitoxin Partner Ph Through Fold Complementation
J. Biol. Chem. V. 283 30821 2008
PubMed-ID: 18757857  |  Reference-DOI: 10.1074/JBC.M805654200

(-) Compounds

Molecule 1 - DEATH ON CURING PROTEIN
    Chains: A, C
    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: DOC
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE P1
    Organism Taxid: 10678
    Synonym: DOC
 
Molecule 2 - PREVENT HOST DEATH PROTEIN
    Chains: B, D
    Engineered: YES
    Fragment: PREVENT HOST DEATH PROTEIN C-TERMINAL DOMAIN, UNP RESIDUES 51-73
    Mutation: YES
    Other Details: PEPTIDE ALTA BIOSCIENCE
    Synonym: PHD
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 18)

Asymmetric Unit (2, 18)
No.NameCountTypeFull Name
1BR16Ligand/IonBROMIDE ION
2MSE2Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2MSE1Mod. Amino AcidSELENOMETHIONINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2MSE1Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREALA C:71 , LYS C:73 , ARG C:74 , ASN D:72BINDING SITE FOR RESIDUE BR C 136
02AC2SOFTWAREALA A:71 , ARG A:74BINDING SITE FOR RESIDUE BR A 136
03AC3SOFTWARETHR A:117 , ARG A:120 , ARG C:85BINDING SITE FOR RESIDUE BR C 137
04AC4SOFTWAREARG A:85 , THR B:62BINDING SITE FOR RESIDUE BR A 139
05AC5SOFTWAREALA B:57 , PHE B:60BINDING SITE FOR RESIDUE BR B 9
06AC6SOFTWAREMET A:26 , ASP A:28 , GLY A:30 , ARG A:31 , ALA A:32BINDING SITE FOR RESIDUE BR A 140
07AC7SOFTWAREARG A:19BINDING SITE FOR RESIDUE BR A 141
08AC8SOFTWAREHIS A:13 , ASP A:14 , PRO A:24 , GLY A:25BINDING SITE FOR RESIDUE BR A 143
09AC9SOFTWAREPHE D:60BINDING SITE FOR RESIDUE BR C 140
10BC1SOFTWAREALA A:71 , ASN A:72BINDING SITE FOR RESIDUE BR A 144
11BC2SOFTWAREASP C:70 , ALA C:71 , ASN C:72BINDING SITE FOR RESIDUE BR C 141

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DD7)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3DD7)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DD7)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIDOPS51459 Fido domain profile.DOC_BPP14-120
 		  2A:4-120
C:4-120
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIDOPS51459 Fido domain profile.DOC_BPP14-120
 		  1A:4-120
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIDOPS51459 Fido domain profile.DOC_BPP14-120
 		  1-
C:4-120

(-) Exons   (0, 0)

(no "Exon" information available for 3DD7)

(-) 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:123
 aligned with DOC_BPP1 | Q06259 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:123
                                    10        20        30        40        50        60        70        80        90       100       110       120   
             DOC_BPP1     1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYG 123
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FIDO  PDB: A:4-120 UniProt: 4-120                                                                                    --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dd7 A   1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGYIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYG 123
                                    10        20        30        40        50        60        70        80        90       100       110       120   


Chain B from PDB  Type:PROTEIN  Length:18
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:18
                                    63        
             PHD_BPP1    54 AEFASLFDTLDSTNKELV  71
               SCOP domains ------------------ SCOP domains
               CATH domains ------------------ CATH domains
               Pfam domains ------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------ SAPs(SNPs)
                    PROSITE ------------------ PROSITE
                 Transcript ------------------ Transcript
                 3dd7 B  54 AEFASLFDTLDSTNKEmV  71
                                    63      | 
                                           70-MSE


Chain C from PDB  Type:PROTEIN  Length:122
 aligned with DOC_BPP1 | Q06259 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:123
                                    10        20        30        40        50        60        70        80        90       100       110       120   
             DOC_BPP1     1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYG 123
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhh.....-..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FIDO  PDB: C:4-120 UniProt: 4-120                                                                                    --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dd7 C   1 MRHISPEELIALHDANISRYGGLPGM-DPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGYIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYG 123
                                    10        20     | |30        40        50        60        70        80        90       100       110       120   
                                                    26 |                                                                                               
                                                      28                                                                                               


Chain D from PDB  Type:PROTEIN  Length:22
 aligned with PHD_BPP1 | Q06253 from UniProtKB/Swiss-Prot  Length:73

    Alignment length:22
                                    60        70  
             PHD_BPP1    51 ALDAEFASLFDTLDSTNKELVN  72
               SCOP domains ---------------------- SCOP domains
               CATH domains ---------------------- CATH domains
               Pfam domains ---------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------- SAPs(SNPs)
                    PROSITE ---------------------- PROSITE
                 Transcript ---------------------- Transcript
                 3dd7 D  51 ALDAEFASLFDTLDSTNKEmVN  72
                                    60        70  
                                              70-MSE
   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 3DD7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DD7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DD7)

(-) Gene Ontology  (13, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,C   (DOC_BPP1 | Q06259)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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).
    GO:0004674    protein serine/threonine kinase activity    Catalysis of the reactions: ATP + protein serine = ADP + protein serine phosphate, and ATP + protein threonine = ADP + protein threonine phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0016310    phosphorylation    The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0006417    regulation of translation    Any process that modulates the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0039604    suppression by virus of host translation    Any process in which a virus prevents or reduces the frequency, rate or extent of translation of host mRNA.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.

Chain B,D   (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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3dd7)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3dd7
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  DOC_BPP1 | Q06259
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PHD_BPP1 | Q06253
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  DOC_BPP1 | Q06259
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PHD_BPP1 | Q06253
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DOC_BPP1 | Q06259: 3dd9 3k33 3kh2
        PHD_BPP1 | Q06253: 3hry 3hs2 3k33 3kh2 4zlx 4zm0 4zm2

(-) Related Entries Specified in the PDB File

3dd9 DOCH66Y DIMER