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(-) Description

Title :  STRUCTURE OF APO HUMAN NEK7
 
Authors :  M. W. Richards, R. Bayliss
Date :  24 Aug 09  (Deposition) - 08 Dec 09  (Release) - 08 Dec 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Atp-Binding, Polymorphism, Metal-Binding, Serine/Threonine-Protein Kinase, Cell Cycle Kinase, Mitosis, Cytoplasm, Magnesium, Transferase, Phosphoprotein, Protein Kinase, Nucleotide-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. W. Richards, L. O'Regan, C. Mas-Droux, J. M. Y. Blot, J. Cheung, S. Hoelder, A. M. Fry, R. Bayliss
An Auto-Inhibitory Tyrosine Motif In The Cell- Cycle Regulated Nek7 Kinase Is Released Through Binding Of Nek9
Mol. Cell V. 36 560 2009
PubMed-ID: 19941817  |  Reference-DOI: 10.1016/J.MOLCEL.2009.09.038

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE NEK7
    ChainsA
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET30
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VariantCODONPLUS RPIL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymNEK7, NIMA-RELATED PROTEIN KINASE 7

 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
1NI1Ligand/IonNICKEL (II) ION
2SO41Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:23 , ARG A:136 , THR A:137 , LYS A:140 , HOH A:2178 , HOH A:2179BINDING SITE FOR RESIDUE SO4 A1301
2AC2SOFTWAREHIS A:209 , CYS A:247BINDING SITE FOR RESIDUE NI A1302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2WQM)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2WQM)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040924R35GNEK7_HUMANPolymorphism55833332AR35G
2UniProtVAR_040925I275MNEK7_HUMANUnclassified  ---AI275M

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.NEK7_HUMAN40-63  1A:40-63
2PROTEIN_KINASE_STPS00108 Serine/Threonine protein kinases active-site signature.NEK7_HUMAN157-169  1A:157-169

(-) Exons   (0, 0)

(no "Exon" information available for 2WQM)

(-) 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:258
 aligned with NEK7_HUMAN | Q8TDX7 from UniProtKB/Swiss-Prot  Length:302

    Alignment length:281
                                    29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299 
           NEK7_HUMAN    20 KALRPDMGYNTLANFRIEKKIGRGQFSEVYRAACLLDGVPVALKKVQIFDLMDAKARADCIKEIDLLKQLNHPNVIKYYASFIEDNELNIVLELADAGDLSRMIKHFKKQKRLIPERTVWKYFVQLCSALEHMHSRRVMHRDIKPANVFITATGVVKLGDLGLGRFFSSKTTAAHSLVGTPYYMSPERIHENGYNFKSDIWSLGCLLYEMAALQSPFYGDKMNLYSLCKKIEQCDYPPLPSDHYSEELRQLVNMCINPDPEKRPDVTYVYDVAKRMHACTA 300
               SCOP domains d2wqma_ A: automated mat  ches                                                                                                                                                                                                                                                            SCOP domains
               CATH domains ------------------------  ---------------------------2wqmA02                -------------------2wqmA02 A:73-95,A:115-300 Transferase(Phosphotransferase) domain 1                                                                                                                         CATH domains
               Pfam domains --------------Pkinase-2w  qmA01 A:34-292                                                                                                                                                                                                                                         -------- Pfam domains
         Sec.struct. author ..........hhh.eeeeee....--.eeeeeee.....eeeeeee......hhhhhhhhhhhhhhhhh........eeeeeee..eeeeeee.....hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhh.......hhhhhee.....ee....------------------.....hhhhhh....hhhhhhhhh.hhhhhhhhh.....---.hhhhhhhhhhh...........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------G-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------M------------------------- SAPs(SNPs)
                    PROSITE --------------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------------PROTEIN_KINAS----------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2wqm A  20 KALRPDMGYNTLANFRIEKKIGRG--SEVYRAACLLDGVPVALKKVQIFDLMDAKARADCIKEIDLLKQLNHPNVIKYYASFIEDNELNIVLELADAGDLSRMIKHFKKQKRLIPERTVWKYFVQLCSALEHMHSRRVMHRDIKPANVFITATGVVKLGDL------------------TPYYMSPERIHENGYNFKSDIWSLGCLLYEMAALQSPFY---MNLYSLCKKIEQCDYPPLPSDHYSEELRQLVNMCINPDPEKRPDVTYVYDVAKRMHACTA 300
                                    29        39   |  | 49        59        69        79        89        99       109       119       129       139       149       159       169       179|        -       199       209       219       229       | - |     249       259       269       279       289       299 
                                                  43 46                                                                                                                                   180                199                                   237 241                                                           

   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  (1, 1)

Asymmetric/Biological Unit

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: PKinase (934)

(-) Gene Ontology  (22, 22)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NEK7_HUMAN | Q8TDX7)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0004672    protein kinase activity    Catalysis of the phosphorylation of an amino acid residue in a protein, usually according to the reaction: a protein + ATP = a phosphoprotein + ADP.
    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:0000910    cytokinesis    The division of the cytoplasm and the plasma membrane of a cell and its partitioning into two daughter cells.
    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:0051973    positive regulation of telomerase activity    Any process that activates or increases the frequency, rate or extent of telomerase activity, the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    GO:1904355    positive regulation of telomere capping    Any process that activates or increases the frequency, rate or extent of telomere capping.
    GO:0032212    positive regulation of telomere maintenance via telomerase    Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0007346    regulation of mitotic cell cycle    Any process that modulates the rate or extent of progress through the mitotic cell cycle.
    GO:0051225    spindle assembly    The aggregation, arrangement and bonding together of a set of components to form the spindle, the array of microtubules and associated molecules that serves to move duplicated chromosomes apart.
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: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:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    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.
    GO:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        NEK7_HUMAN | Q8TDX72wqn 5de2

(-) Related Entries Specified in the PDB File

2wqn STRUCTURE OF ADP-BOUND HUMAN NEK7
2wqo NEK7