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

(-) Description

Title :  MITOCHONDRIAL ADCK3 EMPLOYS AN ATYPICAL PROTEIN KINASE-LIKE FOLD TO ENABLE COENZYME Q BIOSYNTHES
 
Authors :  C. A. Bingman, R. Smith, S. Joshi, J. A. Stefely, A. G. Reidenbach, A. Ulb O. Oruganty, B. J. Floyd, A. Jochem, J. M. Saunders, I. E. Johnson, R. L. G. E. Barber, D. Lee, S. Li, N. Kannan, J. J. Coon, D. J. Pagliarini, Mito Protein Partnership (Mpp)
Date :  23 Apr 14  (Deposition) - 19 Nov 14  (Release) - 21 Jan 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.64
Chains :  Asym./Biol. Unit :  A
Keywords :  Protein Kinase-Like, Coenzyme Q Biosynthesis, Mitochondrial, Membrane Associated, Structural Genomics, Psi-Biology, Mitochondrial Protein Partnership, Mpp, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. A. Stefely, A. G. Reidenbach, A. Ulbrich, K. Oruganty, B. J. Floyd, A. Jochem, J. M. Saunders, I. E. Johnson, C. E. Minogue, R. L. Wrobel, G. E. Barber, D. Lee, S. Li, N. Kannan, J. J. Coon, C. A. Bingman, D. J. Pagliarini
Mitochondrial Adck3 Employs An Atypical Protein Kinase-Like Fold To Enable Coenzyme Q Biosynthesis.
Mol. Cell V. 57 83 2015
PubMed-ID: 25498144  |  Reference-DOI: 10.1016/J.MOLCEL.2014.11.002

(-) Compounds

Molecule 1 - CHAPERONE ACTIVITY OF BC1 COMPLEX-LIKE, MITOCHONDRIAL
    ChainsA
    EC Number2.7.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 204-595
    GeneADCK3, CABC1, PP265
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCHAPERONE-ABC1-LIKE,AARF DOMAIN-CONTAINING PROTEIN KINASE 3

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 17)

Asymmetric/Biological Unit (2, 17)
No.NameCountTypeFull Name
1MSE15Mod. Amino AcidSELENOMETHIONINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:410 , THR A:548 , ARG A:596 , ARG A:598 , LEU A:599 , HOH A:846binding site for residue SO4 A 701
2AC2SOFTWAREASN A:259 , LEU A:459 , SER A:460 , GLN A:461 , ARG A:464 , HOH A:841binding site for residue SO4 A 702

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4PED)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4PED)

(-) Sequences/Alignments

Asymmetric/Biological 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:387
                                                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhh.eeee.....eee..eeeeeeee....eeeeeee...hhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee....hhhhh...eeeee....ee.hhh...hhhhhhhhhhhhhhhhhhhhhh..eee...hhh.eeee....eeee.....eee.hhhhhhhhhhhhhhhhh.hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...ee..hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh..ee.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ped A 258 ANAERIVRTLCKVRGAALKLGQmLSIQDDAFINPHLAKIFERVRQSADFmPLKQmmKTLNNDLGPNWRDKLEYFEERPFAAASIGQVHLARmKGGREVAmKIQYPGVAQSINSDVNNLmAVLNmSNmLPEGLFPEHLIDVLRRELALECDYQREAACARKFRDLLKGHPFFYVPEIVDELCSPHVLTTELVSGFPLDQAEGLSQEIRNEICYNILVLCLRELFEFHFmQTDPNWSNFFYDPQQHKVALLDFGATREYDRSFTDLYIQIIRAAADRDRETVRAKSIEmKFLTGYEVKVmEDAHLDAILILGEAFASDEPFDFGTQSTTEKIHNLIPVmLRHRLVPPPEETYSLHRKmGGSFLICSKLKARFPCKAmFEEAYSNYCKRQ 644
                                   267       277  |    287       297       307    || 317       327       337       347 |     357       367       377   |  |387       397       407       417       427       437       447       457       467       477       487       497       507       517       527       537      |547       557       567       577       587      |597       607     | 617       627    |  637       
                                                280-MSE                    307-MSE||                                 349-MSE 357-MSE            376-MSE|  |                                                                                                  485-MSE                                                    544-MSE    555-MSE                                594-MSE            613-MSE            632-MSE        
                                                                                312-MSE                                                              381-MSE                                                                                                                                                                                                                                                                   
                                                                                 313-MSE                                                                384-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 4PED)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ped)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ped
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  COQ8A_HUMAN | Q8NI60
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.-
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  COQ8A_HUMAN | Q8NI60
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        COQ8A_HUMAN | Q8NI605i35

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4PED)