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(-) Description

Title :  CRYSTAL STRUCTURE OF THE HUMAN KIF9 MOTOR DOMAIN IN COMPLEX WITH ADP
 
Authors :  H. Zhu, W. Tempel, H. He, Y. Shen, J. Wang, G. Brothers, R. Landry, C. H. Ar A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park, Struct Genomics Consortium (Sgc)
Date :  09 Jul 10  (Deposition) - 21 Jul 10  (Release) - 21 Jul 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Kinesin, Motor Domain, Adp, Structural Genomics, Structural Genomics Consortium, Sgc, Contractile Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Zhu, W. Tempel, H. He, Y. Shen, J. Wang, G. Brothers, R. Landry, C. H. Arrowsmith, A. M. Edwards, M. Sundstrom, J. Weigelt, A. Bochkarev, H. Park
Crystal Structure Of The Human Kif9 Motor Domain In Complex With Adp
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - KINESIN-LIKE PROTEIN KIF9
    ChainsA
    EngineeredYES
    Expression SystemTRICHOPLUSIA NI
    Expression System Taxid7111
    Expression System VectorPFBOH-LIC
    FragmentMOTOR DOMAIN (UNP RESIDUES 1-340)
    GeneKIF9
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (3x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric Unit (4, 11)
No.NameCountTypeFull Name
1ADP1Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL1Ligand/IonCHLORIDE ION
3MG1Ligand/IonMAGNESIUM ION
4UNX8Ligand/IonUNKNOWN ATOM OR ION
Biological Unit 1 (2, 27)
No.NameCountTypeFull Name
1ADP3Ligand/IonADENOSINE-5'-DIPHOSPHATE
2CL-1Ligand/IonCHLORIDE ION
3MG-1Ligand/IonMAGNESIUM ION
4UNX24Ligand/IonUNKNOWN ATOM OR ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:100 , HOH A:342 , HOH A:343 , HOH A:344 , HOH A:346 , ADP A:401BINDING SITE FOR RESIDUE MG A 402
2AC2SOFTWARESER A:65 , GLN A:66 , HIS A:112 , HOH A:415BINDING SITE FOR RESIDUE CL A 341
3AC3SOFTWAREARG A:12 , LYS A:14 , PRO A:15 , GLN A:94 , THR A:95 , GLY A:96 , ALA A:97 , GLY A:98 , LYS A:99 , THR A:100 , TYR A:101 , HOH A:342 , HOH A:343 , HOH A:346 , HOH A:347 , HOH A:355 , MG A:402BINDING SITE FOR RESIDUE ADP A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_022139V78IKIF9_HUMANPolymorphism2270569AV78I
2UniProtVAR_020443G96AKIF9_HUMANPolymorphism3733092AG96A

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_022139V78IKIF9_HUMANPolymorphism2270569AV78I
2UniProtVAR_020443G96AKIF9_HUMANPolymorphism3733092AG96A

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

(-) PROSITE Motifs  (2, 2)

Asymmetric Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KIF9_HUMAN6-340  1A:6-340
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KIF9_HUMAN239-250  1A:239-250
Biological Unit 1 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1KINESIN_MOTOR_2PS50067 Kinesin motor domain profile.KIF9_HUMAN6-340  3A:6-340
2KINESIN_MOTOR_1PS00411 Kinesin motor domain signature.KIF9_HUMAN239-250  3A:239-250

(-) Exons   (9, 9)

Asymmetric Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003350442bENSE00001672395chr3:47324337-47323985353KIF9_HUMAN-00--
1.4bENST000003350444bENSE00002170013chr3:47318869-4731877298KIF9_HUMAN1-31311A:5-3127
1.5aENST000003350445aENSE00001792729chr3:47316980-47316815166KIF9_HUMAN32-87561A:32-8756
1.6ENST000003350446ENSE00001080805chr3:47315148-47315042107KIF9_HUMAN87-122361A:87-12236
1.7ENST000003350447ENSE00001080802chr3:47312951-47312727225KIF9_HUMAN123-197751A:123-19775
1.8ENST000003350448ENSE00001080801chr3:47308753-4730867084KIF9_HUMAN198-225281A:198-22528
1.9bENST000003350449bENSE00001080803chr3:47308558-4730846693KIF9_HUMAN226-256311A:226-250 (gaps)25
1.10bENST0000033504410bENSE00001080789chr3:47307367-47307220148KIF9_HUMAN257-306501A:267-306 (gaps)40
1.11aENST0000033504411aENSE00001080799chr3:47305840-4730577665KIF9_HUMAN306-327221A:306-32722
1.12ENST0000033504412ENSE00001767172chr3:47299050-4729897378KIF9_HUMAN328-353261A:328-34013
1.13bENST0000033504413bENSE00001080795chr3:47289576-4728950869KIF9_HUMAN354-376230--
1.14ENST0000033504414ENSE00001756108chr3:47288967-47288863105KIF9_HUMAN377-411350--
1.15ENST0000033504415ENSE00001685861chr3:47287742-4728768756KIF9_HUMAN412-430190--
1.16ENST0000033504416ENSE00001080793chr3:47287001-4728691191KIF9_HUMAN430-460310--
1.17ENST0000033504417ENSE00001080797chr3:47286414-47286281134KIF9_HUMAN461-505450--
1.18ENST0000033504418ENSE00001080792chr3:47284735-47284541195KIF9_HUMAN505-570660--
1.19ENST0000033504419ENSE00001080791chr3:47282505-47282291215KIF9_HUMAN570-642730--
1.21aENST0000033504421aENSE00001080808chr3:47278109-47277933177KIF9_HUMAN642-701600--
1.22ENST0000033504422ENSE00001734314chr3:47277639-47277524116KIF9_HUMAN701-739390--
1.23ENST0000033504423ENSE00001804907chr3:47277107-47277003105KIF9_HUMAN740-774350--
1.24eENST0000033504424eENSE00001593057chr3:47270192-47269516677KIF9_HUMAN775-790160--

(-) 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:308
 aligned with KIF9_HUMAN | Q9HAQ2 from UniProtKB/Swiss-Prot  Length:790

    Alignment length:336
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334      
           KIF9_HUMAN     5 KKVHAFVRVKPTDDFAHEMIRYGDDKRSIDIHLKKDIRRGVVNNQQTDWSFKLDGVLHDASQDLVYETVAKDVVSQALDGYNGTIMCYGQTGAGKTYTMMGATENYKHRGILPRALQQVFRMIEERPTHAITVRVSYLEIYNESLFDLLSTLPYVGPSVTPMTIVENPQGVFIKGLSVHLTSQEEDAFSLLFEGETNRIIASHTMNKNSSRSHCIFTIYLEAHSRTLSEEKYITSKINLVDLAGSERLGKSGSEGQVLKEATYINKSLSFLEQAIIALGDQKRDHIPFRQCKLTHALKDSLGGNCNMVLVTNIYGEAAQLEETLSSLRFASRMKLV 340
               SCOP domains d3nwna_ A: automated matches                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains -------Kinesin-3nwnA01 A:12-340                                                                                                                                                                                                                                                                                                                  Pfam domains
         Sec.struct. author ..eeeeeee..........eee.....eeeee.....hhhhhh....eeeee..eeee..hhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhh....hhhhhhhhhhhhhhhhhhhhh....eeeeeeeeeeee..eeee...............eeeee..eeeee....ee..hhhhhhhhhhhhhhhhhhhhhhhh.hhhhheeeeeeeeeee-------..eeeeeeeee.....----------------...hhhhhhhhhhhhhhh-----.hhhhhhhhhhhhhhhh...eeeeeeee..hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------I-----------------A---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -KINESIN_MOTOR_2  PDB: A:6-340 UniProt: 6-340                                                                                                                                                                                                                                                                                                    PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------KINESIN_MOTO------------------------------------------------------------------------------------------ PROSITE (2)
           Transcript 1 (1) Exon 1.4b  PDB: A:5-31     Exon 1.5a  PDB: A:32-87 UniProt: 32-87                  -----------------------------------Exon 1.7  PDB: A:123-197 UniProt: 123-197                                  Exon 1.8  PDB: A:198-225    Exon 1.9b  PDB: A:226-250 (gapsExon 1.10b  PDB: A:267-306 (gaps) UniProt: 257-306---------------------Exon 1.12     Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------------------------Exon 1.6  PDB: A:87-122             ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.11a            ------------- Transcript 1 (2)
                 3nwn A   5 KKVHAFVRVKPTDDFAHEMIRYGDDKRSIDIHLKKDIRRGVVNNQQTDWSFKLDGVLHDASQDLVYETVAKDVVSQALDGYNGTIMCYGQTGAGKTYTMMGATENYKHRGILPRALQQVFRMIEERPTHAITVRVSYLEIYNESLFDLLSTLPYVGPSVTPMTIVENPQGVFIKGLSVHLTSQEEDAFSLLFEGETNRIIASHTMNKNSSRSHCIFTIYLEAH-------KYITSKINLVDLAGSE----------------YINKSLSFLEQAIIALGD-----IPFRQCKLTHALKDSLGGNCNMVLVTNIYGEAAQLEETLSSLRFASRMKLV 340
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224  |      -|      244     |   -         -  |    274       284     | 294       304       314       324       334      
                                                                                                                                                                                                                                                        227     235            250              267              284   290                                                  

   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 Unit

(-) CATH Domains  (0, 0 ; only for superseded entry 2NR8: 1,1)

(no "CATH Domain" information available for 3NWN, only for superseded entry 2NR8 replaced by 3NWN)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (17, 17)

Asymmetric Unit(hide GO term definitions)
Chain A   (KIF9_HUMAN | Q9HAQ2)
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: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:0046983    protein dimerization activity    The formation of a protein dimer, a macromolecular structure consists of two noncovalently associated identical or nonidentical subunits.
biological process
    GO:0022617    extracellular matrix disassembly    A process that results in the breakdown of the extracellular matrix.
    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:1903008    organelle disassembly    The disaggregation of an organelle into its constituent components.
    GO:0071801    regulation of podosome assembly    Any process that modulates the frequency, rate or extent of podosome assembly.
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.
    GO:0002102    podosome    An actin-rich adhesion structure characterized by formation upon cell substrate contact and localization at the substrate-attached part of the cell, contain an F-actin-rich core surrounded by a ring structure containing proteins such as vinculin and talin, and have a diameter of 0.5 mm.
    GO:0031982    vesicle    Any small, fluid-filled, spherical organelle enclosed by membrane.

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