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 :  CRYSTAL STRUCTURE OF THE DROSOPHILA KINESIN FAMILY MEMBER KIN10/NOD IN COMPLEX WITH DIVALENT MANGANESE AND ADP
 
Authors :  J. C. Cochran, Y. C. Zhao, D. E. Wilcox, F. J. Kull
Date :  10 Dec 10  (Deposition) - 21 Dec 11  (Release) - 27 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym./Biol. Unit :  A
Keywords :  Kinesin, Motor Domain, Atp Hydrolysis, Meiosis, Spindle Protein, Atp- Binding, Cell Cycle, Cell Division, Microtubule, Motor Protein, Nucleotide-Binding, Alpha/Beta Class (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. C. Cochran, Y. C. Zhao, D. E. Wilcox, F. J. Kull
A Metal Switch For Controlling The Activity Of Molecular Motor Proteins.
Nat. Struct. Mol. Biol. V. 19 122 2012
PubMed-ID: 22198464  |  Reference-DOI: 10.1038/NSMB.2190

(-) Compounds

Molecule 1 - KINESIN-LIKE PROTEIN NOD
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 1-322
    GeneNOD, NODA, CG1763
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2MN1Ligand/IonMANGANESE (II) ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:94 , ADP A:401BINDING SITE FOR RESIDUE MN A 402
2AC2SOFTWAREPRO A:17 , THR A:89 , GLY A:90 , THR A:91 , GLY A:92 , LYS A:93 , SER A:94 , TYR A:95 , ASP A:133 , ALA A:134 , LYS A:216 , MN A:402 , HOH A:506 , HOH A:517BINDING SITE FOR RESIDUE ADP A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric/Biological Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_NOD_DROME_001 *S94NNOD_DROME  ---  ---AS94N
   * ID not provided by source

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.NOD_DROME8-320  1A:8-320
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.NOD_DROME220-231  1A:220-231

(-) Exons   (0, 0)

(no "Exon" information available for 3PXN)

(-) 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:291
 aligned with NOD_DROME | P18105 from UniProtKB/Swiss-Prot  Length:666

    Alignment length:321
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323 
            NOD_DROME     4 AKLSAVRIAVREAPYRQFLGRREPSVVQFPPWSDGKSLIVDQNEFHFDHAFPATISQDEMYQALILPLVDKLLEGFQCTALAYGQTGTGKSYSMGMTPPGEILPEHLGILPRALGDIFERVTARQENNKDAIQVYASFIEIYNEKPFDLLGSTPHMPMVAARCQRCTCLPLHSQADLHHILELGTRNRRVRPTNMNSNSSRSHAIVTIHVKSKTHHSRMNIVDLAGSEGVRRTGHEGVARQEGVNINLGLLSINKVVMSMAAGHTVIPYRDSVLTTVLQASLTAQSYLTFLACISPHQCDLSETLSTLRFGTSAKKLRLNP 324
               SCOP domains d3pxna_ A: autom       ated matches                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee....-------.............eeee..eeee..eee....hhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh........eeeeeeeeeee...eee....................ee..hhhhhhhhhhhhhhh..----------..eeeeeeeeeee...eeeeeeee.......-------------...hhhhhhhhhhhhhhh......hhhhhhhhhhh........eeeeeeee..hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------N-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----KINESIN_MOTOR_2  PDB: A:8-320 UniProt: 8-320                                                                                                                                                                                                                                                                             ---- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO--------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pxn A   4 AKLSAVRIAVREAPYR-------PSVVQFPPWSDGKSLIVDQNEFHFDHAFPATISQDEMYQALILPLVDKLLEGFQCTALAYGQTGTGKSYSMGMTPPGEILPEHLGILPRALGDIFERVTARQENNKDAIQVYASFIEIYNEKPFDLLGSTPHMPMVAARCQRCTCLPLHSQADLHHILELGTRNRR----------SRSHAIVTIHVKSKTHHSRMNIVDLAGSEGV-------------VNINLGLLSINKVVMSMAAGHTVIPYRDSVLTTVLQASLTAQSYLTFLACISPHQCDLSETLSTLRFGTSAKKLRLEH 324
                                    13     |   -   |    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183        |-       203       213       223       233         -   |   253       263       273       283       293       303       313       323 
                                          19      27                                                                                                                                                                  192        203                           233           247                                                                             

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NOD_DROME | P18105)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0008017    microtubule binding    Interacting selectively and non-covalently with microtubules, filaments composed of tubulin monomers.
    GO:0003777    microtubule motor activity    Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
    GO:0051010    microtubule plus-end binding    Interacting selectively and non-covalently with the plus end of a microtubule.
    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.
biological process
    GO:0032837    distributive segregation    The cell cycle process in which genetic material, in the form of chromosomes, is organized and then physically separated and apportioned to two or more sets during a normally chiasmate meiosis under the condition that chiasma have not occurred between a particular pair of homologs. Distributive segregation is a "backup" mechanism to ensure the segregation of homologs that have failed to cross over - either as a consequence of mutation or not, as, for example, the 4th chromosome of Drosophila melanogaster (which never exchanges, presumably due to its small size) - but nevertheless segregate normally.
    GO:0051296    establishment of meiotic spindle orientation    Any process that set the alignment of meiotic spindle relative to other cellular structures.
    GO:0007143    female meiotic nuclear division    A cell cycle process by which the cell nucleus divides as part of a meiotic cell cycle in the female germline.
    GO:0045132    meiotic chromosome segregation    The process in which genetic material, in the form of chromosomes, is organized into specific structures and then physically separated and apportioned to two or more sets during M phase of the meiotic cell cycle.
    GO:0007018    microtubule-based movement    A microtubule-based process that results in the movement of organelles, other microtubules, or other cellular components. Examples include motor-driven movement along microtubules and movement driven by polymerization or depolymerization of microtubules.
    GO:0007052    mitotic spindle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
    GO:0031116    positive regulation of microtubule polymerization    Any process that activates or increases the frequency, rate or extent of microtubule polymerization.
    GO:0007057    spindle assembly involved in female meiosis I    The aggregation, arrangement and bonding together of a set of components to form the spindle during meiosis I of a meiotic cell cycle in females. An example of this is found in Drosophila melanogaster.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    GO:0005871    kinesin complex    Any complex that includes a dimer of molecules from the kinesin superfamily, a group of related proteins that contain an extended region of predicted alpha-helical coiled coil in the main chain that likely produces dimerization. The native complexes of several kinesin family members have also been shown to contain additional peptides, often designated light chains as all of the noncatalytic subunits that are currently known are smaller than the chain that contains the motor unit. Kinesin complexes generally possess a force-generating enzymatic activity, or motor, which converts the free energy of the gamma phosphate bond of ATP into mechanical work.
    GO:0005874    microtubule    Any of the long, generally straight, hollow tubes of internal diameter 12-15 nm and external diameter 24 nm found in a wide variety of eukaryotic cells; each consists (usually) of 13 protofilaments of polymeric tubulin, staggered in such a manner that the tubulin monomers are arranged in a helical pattern on the microtubular surface, and with the alpha/beta axes of the tubulin subunits parallel to the long axis of the tubule; exist in equilibrium with pool of tubulin monomers and can be rapidly assembled or disassembled in response to physiological stimuli; concerned with force generation, e.g. in the spindle.

 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
    ADP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3pxn)
 

(-) 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
  3pxn
    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
  NOD_DROME | P18105
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  NOD_DROME | P18105
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NOD_DROME | P181053dc4 3dcb 3dco

(-) Related Entries Specified in the PDB File

3dc4 NOD-MGADP
3dcb NOD-MGAMPPNP
3dco MT-NOD (NUCLEOTIDE-FREE)