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(-) Description

Title :  STRUCTURE OF DOCH66Y DIMER
 
Authors :  A. Garcia-Pino, R. Loris
Date :  05 Jun 08  (Deposition) - 09 Jun 09  (Release) - 23 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.45
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  All Alpha, Ribosome Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Garcia-Pino, M. Christensen-Dalsgaard, L. Wyns, M. B. Yarmolinky R. D. Magnusson, K. Gerdes, R. Loris
Doc Of Phage P1 Adopts An Incomplete Fic Fold That Is Complemented By Its Antitoxin Phd
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DEATH ON CURING 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: DOC
    Mutation: YES
    Organism Scientific: ENTEROBACTERIA PHAGE P1
    Organism Taxid: 10678

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3DD9)

(-) Sites  (0, 0)

(no "Site" information available for 3DD9)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3DD9)

(-) Cis Peptide Bonds  (11, 11)

Asymmetric Unit
No.Residues
1Asp A:28 -Pro A:29
2Pro A:29 -Gly A:30
3Gly B:65 -Tyr B:66
4Ala C:44 -Tyr C:45
5Glu C:47 -Ile C:48
6Ser C:124 -Ala C:125
7Gly D:65 -Tyr D:66
8Arg E:64 -Gly E:65
9Pro F:29 -Gly F:30
10Pro G:29 -Gly G:30
11Gly G:30 -Arg G:31

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3DD9)

(-) PROSITE Motifs  (1, 8)

Asymmetric Unit (1, 8)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIDOPS51459 Fido domain profile.DOC_BPP14-120
 
 
 
 
 
 
 		  8A:4-120
B:4-120
C:4-120
D:4-120
E:4-120
F:4-120
G:4-120
H:4-120
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIDOPS51459 Fido domain profile.DOC_BPP14-120
 
 
 
 
 
 
 		  2A:4-120
B:4-120
-
-
-
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIDOPS51459 Fido domain profile.DOC_BPP14-120
 
 
 
 
 
 
 		  2-
-
C:4-120
D:4-120
-
-
-
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIDOPS51459 Fido domain profile.DOC_BPP14-120
 
 
 
 
 
 
 		  2-
-
-
-
E:4-120
F:4-120
-
-
Biological Unit 4 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1FIDOPS51459 Fido domain profile.DOC_BPP14-120
 
 
 
 
 
 
 		  2-
-
-
-
-
-
G:4-120
H:4-120

(-) Exons   (0, 0)

(no "Exon" information available for 3DD9)

(-) 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:117
 aligned with DOC_BPP1 | Q06259 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
             DOC_BPP1     1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGSA 125
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh.--------..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FIDO  PDB: A:4-120 UniProt: 4-120                                                                                    ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dd9 A   1 MRHISPEELIALHDANISR--------DPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGYIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGSA 125
                                    10        |-       |30        40        50        60        70        80        90       100       110       120     
                                             19       28                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:118
 aligned with DOC_BPP1 | Q06259 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
             DOC_BPP1     1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGS 124
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh------..hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FIDO  PDB: B:4-120 UniProt: 4-120                                                                                    ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dd9 B   1 MRHISPEELIALHDANISRY------SDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGYIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGS 124
                                    10        20      | 30        40        50        60        70        80        90       100       110       120    
                                              20     27                                                                                                 


Chain C from PDB  Type:PROTEIN  Length:115
 aligned with DOC_BPP1 | Q06259 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:125
                                    10        20        30        40        50        60        70        80        90       100       110       120     
             DOC_BPP1     1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGSA 125
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.----------.hhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FIDO  PDB: C:4-120 UniProt: 4-120                                                                                    ----- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dd9 C   1 MRHISPEELIALHDANIS----------PGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGYIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGSA 125
                                    10       | -        30        40        50        60        70        80        90       100       110       120     
                                            18         29                                                                                                


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

    Alignment length:126
                                    10        20        30        40        50        60        70        80        90       100       110       120      
             DOC_BPP1     1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGSAE 126
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhh.----..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh..hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ---FIDO  PDB: D:4-120 UniProt: 4-120                                                                                    ------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3dd9 D   1 MRHISPEELIALHDANISRYG----MSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGYIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGSAD 126
                                    10        20|    |  30        40        50        60        70        80        90       100       110       120      
                                               21   26                                                                                                    


Chain E from PDB  Type:PROTEIN  Length:113
 aligned with DOC_BPP1 | Q06259 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
             DOC_BPP1     1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGS 124
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhh.-----------...hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FIDO  PDB: E:4-120 UniProt: 4-120                                                                                    ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dd9 E   1 MRHISPEELIALHDANIS-----------GRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGYIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGS 124
                                    10       | -        30        40        50        60        70        80        90       100       110       120    
                                            18          30                                                                                              


Chain F from PDB  Type:PROTEIN  Length:110
 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 ....hhhhhhhhhh.-------------.hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FIDO  PDB: F:4-120 UniProt: 4-120                                                                                    --- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dd9 F   1 MRHISPEELIALHDA-------------PGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGYIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYG 123
                                    10    |    -        30        40        50        60        70        80        90       100       110       120   
                                         15            29                                                                                              


Chain G from PDB  Type:PROTEIN  Length:114
 aligned with DOC_BPP1 | Q06259 from UniProtKB/Swiss-Prot  Length:126

    Alignment length:124
                                    10        20        30        40        50        60        70        80        90       100       110       120    
             DOC_BPP1     1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGS 124
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhh----------..hhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhh...hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FIDO  PDB: G:4-120 UniProt: 4-120                                                                                    ---- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dd9 G   1 MRHISPEELIALHDANIS----------PGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGYIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGS 124
                                    10       | -        30        40        50        60        70        80        90       100       110       120    
                                            18         29                                                                                               


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

    Alignment length:129
                                                                                                                                                       126   
                                    10        20        30        40        50        60        70        80        90       100       110       120     |   
             DOC_BPP1     1 MRHISPEELIALHDANISRYGGLPGMSDPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGHIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGSAE---   -
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh.-------.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh..hhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---FIDO  PDB: H:4-120 UniProt: 4-120                                                                                    --------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3dd9 H   1 MRHISPEELIALHDANISRY-------DPGRAEAIIGRVQARVAYEEITDLFEVSATYLVATARGYIFNDANKRTALNSALLFLRRNGVQVFDSPELADLTVGAATGEISVSSVADTLRRLYGSADPLE 129
                                    10        20       |30        40        50        60        70        80        90       100       110       120         
                                              20      28
   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 3DD9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3DD9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3DD9)

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H   (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.

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  Cis Peptide Bonds
    Ala C:44 - Tyr C:45   [ RasMol ]  
    Arg E:64 - Gly E:65   [ RasMol ]  
    Asp A:28 - Pro A:29   [ RasMol ]  
    Glu C:47 - Ile C:48   [ RasMol ]  
    Gly B:65 - Tyr B:66   [ RasMol ]  
    Gly D:65 - Tyr D:66   [ RasMol ]  
    Gly G:30 - Arg G:31   [ RasMol ]  
    Pro A:29 - Gly A:30   [ RasMol ]  
    Pro F:29 - Gly F:30   [ RasMol ]  
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    Ser C:124 - Ala C:125   [ RasMol ]  
 
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  3dd9
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  DOC_BPP1 | Q06259
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 Related Entries

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

UniProtKB/Swiss-Prot
        DOC_BPP1 | Q06259: 3dd7 3k33 3kh2

(-) Related Entries Specified in the PDB File

3dd7 DOCH66Y IN COMPLEX WITH THE C-TERMINUS DOMAIN OF PHD