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(-) Description

Title :  INSIGHTS INTO DYNEIN ASSEMBLY FROM A DYNEIN INTERMEDIATE CHAIN-LIGHT CHAIN ROADBLOCK STRUCTURE
 
Authors :  J. Hall, P. A. Karplus, E. Barbar
Date :  05 Jan 10  (Deposition) - 12 May 10  (Release) - 18 Sep 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.00
Chains :  Asym. Unit :  A,B,C,D,W,X,Y,Z
Biol. Unit 1:  A,Y  (1x)
Biol. Unit 2:  B,Z  (1x)
Biol. Unit 3:  C,W  (1x)
Biol. Unit 4:  D,X  (1x)
Biol. Unit 5:  A,B,Y,Z  (1x)
Biol. Unit 6:  C,D,W,X  (1x)
Keywords :  Dynein, Intermediate Chain, Ic, Lc7, Light Chain 7, Km23, Roadblock, Hydrolase, Lysosome, Membrane, Microtubule, Motor Protein, Nucleus, Wd Repeat (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Hall, P. A. Karplus, E. Barbar
Insights Into Dynein Assembly From A Dynein Intermediate Chain-Light Chain Roadblock Structure
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - RE64145P
    ChainsA, B, C, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15DA
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneROBL, CG10751, DMEL_CG10751
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymROADBLOCK
 
Molecule 2 - DYNEIN INTERMEDIATE CHAIN, CYTOSOLIC
    ChainsW, X, Y, Z
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET15DA
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneSW, CDIC, DIC19B, CG18000
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymDH IC, CYTOPLASMIC DYNEIN INTERMEDIATE CHAIN, PROTEIN SHORT WING

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit ABCDWXYZ
Biological Unit 1 (1x)A     Y 
Biological Unit 2 (1x) B     Z
Biological Unit 3 (1x)  C W   
Biological Unit 4 (1x)   D X  
Biological Unit 5 (1x)AB    YZ
Biological Unit 6 (1x)  CDWX  

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 3L9K)

(-) Sites  (0, 0)

(no "Site" information available for 3L9K)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3L9K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3L9K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3L9K)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3L9K)

(-) Exons   (0, 0)

(no "Exon" information available for 3L9K)

(-) 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:95
 aligned with Q7KMS3_DROME | Q7KMS3 from UniProtKB/TrEMBL  Length:97

    Alignment length:95
                                    12        22        32        42        52        62        72        82        92     
         Q7KMS3_DROME     3 QEVEETLKRIQSHKGVVGTIVVNNEGIPVKSTLDNTTTVQYAGLMSQLADKARSVVRDLDPSNDMTFLRVRSKKHEIMVAPDKDFILIVIQNPTD  97
               SCOP domains d3l9ka_ A: automated matches                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...eeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...eeeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 3l9k A   3 QEVEETLKRIQSHKGVVGTIVVNNEGIPVKSTLDNTTTVQYAGLMSQLADKARSVVRDLDPSNDMTFLRVRSKKHEIMVAPDKDFILIVIQNPTD  97
                                    12        22        32        42        52        62        72        82        92     

Chain B from PDB  Type:PROTEIN  Length:95
 aligned with Q7KMS3_DROME | Q7KMS3 from UniProtKB/TrEMBL  Length:97

    Alignment length:95
                                    12        22        32        42        52        62        72        82        92     
         Q7KMS3_DROME     3 QEVEETLKRIQSHKGVVGTIVVNNEGIPVKSTLDNTTTVQYAGLMSQLADKARSVVRDLDPSNDMTFLRVRSKKHEIMVAPDKDFILIVIQNPTD  97
               SCOP domains d3l9kb_ B: automated matches                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...eeeeeeee....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...eeeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 3l9k B   3 QEVEETLKRIQSHKGVVGTIVVNNEGIPVKSTLDNTTTVQYAGLMSQLADKARSVVRDLDPSNDMTFLRVRSKKHEIMVAPDKDFILIVIQNPTD  97
                                    12        22        32        42        52        62        72        82        92     

Chain C from PDB  Type:PROTEIN  Length:95
 aligned with Q7KMS3_DROME | Q7KMS3 from UniProtKB/TrEMBL  Length:97

    Alignment length:95
                                    12        22        32        42        52        62        72        82        92     
         Q7KMS3_DROME     3 QEVEETLKRIQSHKGVVGTIVVNNEGIPVKSTLDNTTTVQYAGLMSQLADKARSVVRDLDPSNDMTFLRVRSKKHEIMVAPDKDFILIVIQNPTD  97
               SCOP domains d3l9kc_ C: automated matches                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...eeeeeeee..........hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...eeeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 3l9k C   3 QEVEETLKRIQSHKGVVGTIVVNNEGIPVKSTLDNTTTVQYAGLMSQLADKARSVVRDLDPSNDMTFLRVRSKKHEIMVAPDKDFILIVIQNPTD  97
                                    12        22        32        42        52        62        72        82        92     

Chain D from PDB  Type:PROTEIN  Length:95
 aligned with Q7KMS3_DROME | Q7KMS3 from UniProtKB/TrEMBL  Length:97

    Alignment length:95
                                    12        22        32        42        52        62        72        82        92     
         Q7KMS3_DROME     3 QEVEETLKRIQSHKGVVGTIVVNNEGIPVKSTLDNTTTVQYAGLMSQLADKARSVVRDLDPSNDMTFLRVRSKKHEIMVAPDKDFILIVIQNPTD  97
               SCOP domains d3l9kd_ D: automated matches                                                                    SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Robl_LC7-3l9kD01 D:4-94                                                                    --- Pfam domains (1)
           Pfam domains (2) -Robl_LC7-3l9kD02 D:4-94                                                                    --- Pfam domains (2)
           Pfam domains (3) -Robl_LC7-3l9kD03 D:4-94                                                                    --- Pfam domains (3)
           Pfam domains (4) -Robl_LC7-3l9kD04 D:4-94                                                                    --- Pfam domains (4)
         Sec.struct. author ..hhhhhhhhhh...eeeeeeee....eeee..hhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeeeee...eeeeee...eeeeeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------- Transcript
                 3l9k D   3 QEVEETLKRIQSHKGVVGTIVVNNEGIPVKSTLDNTTTVQYAGLMSQLADKARSVVRDLDPSNDMTFLRVRSKKHEIMVAPDKDFILIVIQNPTD  97
                                    12        22        32        42        52        62        72        82        92     

Chain W from PDB  Type:PROTEIN  Length:38
 aligned with DYIN_DROME | Q24246 from UniProtKB/Swiss-Prot  Length:663

    Alignment length:38
                                   251       261       271        
           DYIN_DROME   242 LSEEQKQMIILSENFQRFVVRAGRVIERALSENVDIYT 279
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 3l9k W 221 LSEEQKQMIILSENFQRFVVRAGRVIERALSENVDIYT 258
                                   230       240       250        

Chain X from PDB  Type:PROTEIN  Length:38
 aligned with DYIN_DROME | Q24246 from UniProtKB/Swiss-Prot  Length:663

    Alignment length:38
                                   251       261       271        
           DYIN_DROME   242 LSEEQKQMIILSENFQRFVVRAGRVIERALSENVDIYT 279
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 3l9k X 221 LSEEQKQMIILSENFQRFVVRAGRVIERALSENVDIYT 258
                                   230       240       250        

Chain Y from PDB  Type:PROTEIN  Length:38
 aligned with DYIN_DROME | Q24246 from UniProtKB/Swiss-Prot  Length:663

    Alignment length:38
                                   251       261       271        
           DYIN_DROME   242 LSEEQKQMIILSENFQRFVVRAGRVIERALSENVDIYT 279
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 3l9k Y 221 LSEEQKQMIILSENFQRFVVRAGRVIERALSENVDIYT 258
                                   230       240       250        

Chain Z from PDB  Type:PROTEIN  Length:38
 aligned with DYIN_DROME | Q24246 from UniProtKB/Swiss-Prot  Length:663

    Alignment length:38
                                   251       261       271        
           DYIN_DROME   242 LSEEQKQMIILSENFQRFVVRAGRVIERALSENVDIYT 279
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 3l9k Z 221 LSEEQKQMIILSENFQRFVVRAGRVIERALSENVDIYT 258
                                   230       240       250        

   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, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3L9K)

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: PF (25)

(-) Gene Ontology  (36, 40)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (Q7KMS3_DROME | Q7KMS3)
molecular function
    GO:0016887    ATPase activity    Catalysis of the reaction: ATP + H2O = ADP + phosphate + 2 H+. May or may not be coupled to another reaction.
    GO:0042623    ATPase activity, coupled    Catalysis of the reaction: ATP + H2O = ADP + phosphate; this reaction directly drives some other reaction, for example ion transport across a membrane.
    GO:0045505    dynein intermediate chain binding    Interacting selectively and non-covalently with an intermediate chain of the dynein complex.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
biological process
    GO:0048813    dendrite morphogenesis    The process in which the anatomical structures of a dendrite are generated and organized. A dendrite is a freely branching protoplasmic process of a nerve cell.
    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:0016319    mushroom body development    The process whose specific outcome is the progression of the mushroom body over time, from its formation to the mature structure. The mushroom body is composed of the prominent neuropil structures of the insect central brain, thought to be crucial for olfactory associated learning. These consist mainly of a bulbous calyx and tightly packaged arrays of thin parallel fibers of the Kenyon cells.
cellular component
    GO:0005858    axonemal dynein complex    A dynein complex found in eukaryotic cilia and flagella; the motor domain heads interact with adjacent microtubules to generate a sliding force which is converted to a bending motion.
    GO:0005868    cytoplasmic dynein complex    Any dynein complex with a homodimeric dynein heavy chain core that catalyzes movement along a microtubule. Cytoplasmic dynein complexes participate in many cytoplasmic transport activities in eukaryotes, such as mRNA localization, intermediate filament transport, nuclear envelope breakdown, apoptosis, transport of centrosomal proteins, mitotic spindle assembly, virus transport, kinetochore functions, and movement of signaling and spindle checkpoint proteins. Some complexes participate in intraflagellar transport. Subunits associated with the dynein heavy chain mediate association between dynein heavy chain and cargoes, and may include light chains and light intermediate chains.
    GO:0030286    dynein complex    Any of several large complexes that contain two or three dynein heavy chains and several light chains, and have microtubule motor activity.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.

Chain W,X,Y,Z   (DYIN_DROME | Q24246)
molecular function
    GO:0070840    dynein complex binding    Interacting selectively and non-covalently with a dynein complex, a protein complex that contains two or three dynein heavy chains and several light chains, and has microtubule motor activity.
    GO:0045504    dynein heavy chain binding    Interacting selectively and non-covalently with a heavy chain of the dynein complex.
    GO:0045503    dynein light chain binding    Interacting selectively and non-covalently with a light chain of the dynein complex.
    GO:0003777    microtubule motor activity    Catalysis of movement along a microtubule, coupled to the hydrolysis of a nucleoside triphosphate (usually ATP).
    GO:0003774    motor activity    Catalysis of the generation of force resulting either in movement along a microfilament or microtubule, or in torque resulting in membrane scission, coupled to the hydrolysis of a nucleoside triphosphate.
biological process
    GO:0008088    axo-dendritic transport    The directed movement of organelles or molecules along microtubules in neuron projections.
    GO:0007349    cellularization    The separation of a multi-nucleate cell or syncytium into individual cells. An example of this is found in Drosophila melanogaster embryo development.
    GO:0051642    centrosome localization    Any process in which a centrosome is transported to, and/or maintained in, a specific location within the cell.
    GO:0016482    cytosolic transport    The directed movement of substances or organelles within the cytosol.
    GO:0001754    eye photoreceptor cell differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a photoreceptor cell, as found in the eye, the primary visual organ of most organisms.
    GO:0000226    microtubule cytoskeleton organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising microtubules and their associated proteins.
    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:0034501    protein localization to kinetochore    Any process in which a protein is transported to, or maintained at, the kinetochore.
    GO:0007291    sperm individualization    The resolution of the male germline syncytium or cyst into individual gametes by packaging each spermatid into its own plasma membrane.
    GO:0007051    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 spindle, the array of microtubules and associated molecules that forms between opposite poles of a eukaryotic cell during DNA segregation and serves to move the duplicated chromosomes apart.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005868    cytoplasmic dynein complex    Any dynein complex with a homodimeric dynein heavy chain core that catalyzes movement along a microtubule. Cytoplasmic dynein complexes participate in many cytoplasmic transport activities in eukaryotes, such as mRNA localization, intermediate filament transport, nuclear envelope breakdown, apoptosis, transport of centrosomal proteins, mitotic spindle assembly, virus transport, kinetochore functions, and movement of signaling and spindle checkpoint proteins. Some complexes participate in intraflagellar transport. Subunits associated with the dynein heavy chain mediate association between dynein heavy chain and cargoes, and may include light chains and light intermediate chains.
    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:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0030286    dynein complex    Any of several large complexes that contain two or three dynein heavy chains and several light chains, and have microtubule motor activity.
    GO:0005765    lysosomal membrane    The lipid bilayer surrounding the lysosome and separating its contents from the cell cytoplasm.
    GO:0005764    lysosome    A small lytic vacuole that has cell cycle-independent morphology and is found in most animal cells and that contains a variety of hydrolases, most of which have their maximal activities in the pH range 5-6. The contained enzymes display latency if properly isolated. About 40 different lysosomal hydrolases are known and lysosomes have a great variety of morphologies and functions.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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.
    GO:0005875    microtubule associated complex    Any multimeric complex connected to a microtubule.
    GO:0043005    neuron projection    A prolongation or process extending from a nerve cell, e.g. an axon or dendrite.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DYIN_DROME | Q242462p2t 3fm7
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        Q7KMS3_DROME | Q7KMS33l7h

(-) Related Entries Specified in the PDB File

3l7h APO-LC7 VERSION