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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SERINE/THREONINE-PROTEIN KINASE MST4 IN COMPLEX WITH AN QUINAZOLIN
 
Authors :  A. Chaikuad, P. Rellos, S. Eidarus, S. Das, A. C. W. Pike, R. Sethi, O. Fed P. Savitsky, A. K. Roos, P. Filippakopoulos, C. H. Arrowsmith, A. M. Ed J. Weigelt, C. Bountra, F. Von Delft, S. Knapp, Structural Genomics Consortium (Sgc)
Date :  27 Feb 09  (Deposition) - 24 Mar 09  (Release) - 22 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (1x)
Keywords :  Serine/Threonine-Protein Kinase, Structural Genomics, Structural Genomics Consortium, Sgc, Apoptosis, Atp-Binding, Golgi Apparatus, Kinase, Magnesium, Metal-Binding, Nucleotide-Binding, Phosphoprotein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. J. Record, A. Chaikuad, P. Rellos, S. Das, A. C. Pike, O. Fedorov, B. D. Marsden, S. Knapp, W. H. Lee
Structural Comparison Of Human Mammalian Ste20-Like Kinases
Plos One V. 5 E1190 2010
PubMed-ID: 20730082  |  Reference-DOI: 10.1371/JOURNAL.PONE.0011905

(-) Compounds

Molecule 1 - SERINE/THREONINE-PROTEIN KINASE MST4
    ChainsA, B
    EC Number2.7.11.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3-PRARE2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPROTEIN KINASE
    GeneMST4, MASK
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMAMMALIAN STE20-LIKE PROTEIN KINASE 4, STE20-LIKE KINASE MST4, MST-4, SERINE/THREONINE-PROTEIN KINASE MASK, MST3 AND SOK1- RELATED KINASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B
Biological Unit 3 (1x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
1CD7Ligand/IonCADMIUM ION
2GVD2Ligand/Ion[4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2GVD1Ligand/Ion[4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2GVD1Ligand/Ion[4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1CD-1Ligand/IonCADMIUM ION
2GVD2Ligand/Ion[4-({4-[(5-CYCLOPROPYL-1H-PYRAZOL-3-YL)AMINO]QUINAZOLIN-2-YL}IMINO)CYCLOHEXA-2,5-DIEN-1-YL]ACETONITRILE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:70 , HIS A:142 , VAL A:165 , HOH A:306BINDING SITE FOR RESIDUE CD A 301
2AC2SOFTWARECYS A:77 , HIS A:136 , GLU A:138 , ASP A:242BINDING SITE FOR RESIDUE CD A 302
3AC3SOFTWAREGLU A:267 , SER A:300 , HOH A:307BINDING SITE FOR RESIDUE CD A 303
4AC4SOFTWAREASP A:109 , GVD A:305 , HOH A:359 , HOH A:360BINDING SITE FOR RESIDUE CD A 304
5AC5SOFTWAREILE A:30 , ALA A:51 , LYS A:53 , MET A:99 , GLU A:100 , TYR A:101 , LEU A:102 , ASP A:109 , ALA A:148 , ASN A:149 , LEU A:151 , CD A:304BINDING SITE FOR RESIDUE GVD A 305
6AC6SOFTWAREGLU B:70 , HIS B:142 , VAL B:165 , HOH B:305BINDING SITE FOR RESIDUE CD B 301
7AC7SOFTWARECYS B:77 , HIS B:136 , GLU B:138 , ASP B:242BINDING SITE FOR RESIDUE CD B 302
8AC8SOFTWAREILE B:30 , ASP B:109 , GVD B:304 , HOH B:357BINDING SITE FOR RESIDUE CD B 303
9AC9SOFTWAREILE B:30 , VAL B:38 , ALA B:51 , MET B:99 , GLU B:100 , TYR B:101 , LEU B:102 , ASP B:109 , ALA B:148 , LEU B:151 , CD B:303BINDING SITE FOR RESIDUE GVD B 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 4)

Asymmetric Unit (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040845G36WSTK26_HUMANUnclassified  ---A/BG36W
2UniProtVAR_040846R45CSTK26_HUMANPolymorphism56044451A/BR45C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040845G36WSTK26_HUMANUnclassified  ---AG36W
2UniProtVAR_040846R45CSTK26_HUMANPolymorphism56044451AR45C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040845G36WSTK26_HUMANUnclassified  ---BG36W
2UniProtVAR_040846R45CSTK26_HUMANPolymorphism56044451BR45C

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (2, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_040845G36WSTK26_HUMANUnclassified  ---A/BG36W
2UniProtVAR_040846R45CSTK26_HUMANPolymorphism56044451A/BR45C

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

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.STK26_HUMAN30-53
 
  2A:30-53
B:30-53
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.STK26_HUMAN30-53
 
  1A:30-53
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.STK26_HUMAN30-53
 
  1-
B:30-53
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PROTEIN_KINASE_ATPPS00107 Protein kinases ATP-binding region signature.STK26_HUMAN30-53
 
  2A:30-53
B:30-53

(-) Exons   (0, 0)

(no "Exon" information available for 3GGF)

(-) 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:275
 aligned with STK26_HUMAN | Q9P289 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:284
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    
          STK26_HUMAN    17 IADPEELFTKLERIGKGSFGEVFKGIDNRTQQVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSSYVTKYYGSYLKGSKLWIIMEYLGGGSALDLLRAGPFDEFQIATMLKEILKGLDYLHSEKKIHRDIKAANVLLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIQQSAYDSKADIWSLGITAIELAKGEPPNSDMHPMRVLFLIPKNNPPTLVGDFTKSFKEFIDACLNKDPSFRPTAKELLKHKFIVKNSKKTSYLTELIDRFKRWKAEGHS 300
               SCOP domains d3ggfa_ A: automated matches                                                                                                                                                                                                                                                                 SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhheeeeeeeee...eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhh.........eeeeeee..eeeeeee....eehhhhhh....hhhhhhhhhhhhhhhhh.......ee...hhh.eee.....eee...ee.---------...........hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------W--------C--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------PROTEIN_KINASE_ATP      ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ggf A  17 IADPEELFTKLERIGKGSFGEVFKGIDNRTQQVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSSYVTKYYGSYLKGSKLWIIMEYLGGGSALDLLRAGPFDEFQIATMLKEILKGLDYLHSEKKIHRDIKAANVLLSEQGDVKLADFGVA---------RNTFVGTPFWMAPEVIQQSAYDSKADIWSLGITAIELAKGEPPNSDMHPMRVLFLIPKNNPPTLVGDFTKSFKEFIDACLNKDPSFRPTAKELLKHKFIVKNSKKTSYLTELIDRFKRWKAEGHS 300
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296    
                                                                                                                                                                               166       176                                                                                                                            

Chain B from PDB  Type:PROTEIN  Length:270
 aligned with STK26_HUMAN | Q9P289 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:280
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297
          STK26_HUMAN    18 ADPEELFTKLERIGKGSFGEVFKGIDNRTQQVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSSYVTKYYGSYLKGSKLWIIMEYLGGGSALDLLRAGPFDEFQIATMLKEILKGLDYLHSEKKIHRDIKAANVLLSEQGDVKLADFGVAGQLTDTQIKRNTFVGTPFWMAPEVIQQSAYDSKADIWSLGITAIELAKGEPPNSDMHPMRVLFLIPKNNPPTLVGDFTKSFKEFIDACLNKDPSFRPTAKELLKHKFIVKNSKKTSYLTELIDRFKRWKAE 297
               SCOP domains d3ggfb_ B: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhheeeeeeeee...eeeeeeee.....eeeeeeee.....hhhhhhhhhhhhhh.........eeeeeee..eeeeee.....eehhhhhh....hhhhhhhhhhhhhhhhh.......ee...hhh.eee.....eee...ee.----------..........hhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhh............hhhhhhhhhhhh..hhhhh.hhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------W--------C------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------PROTEIN_KINASE_ATP      ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ggf B  18 ADPEELFTKLERIGKGSFGEVFKGIDNRTQQVVAIKIIDLEEAEDEIEDIQQEITVLSQCDSSYVTKYYGSYLKGSKLWIIMEYLGGGSALDLLRAGPFDEFQIATMLKEILKGLDYLHSEKKIHRDIKAANVLLSEQGDVKLADFGVA----------NTFVGTPFWMAPEVIQQSAYDSKADIWSLGITAIELAKGEPPNSDMHPMRVLFLIPKNNPPTLVGDFTKSFKEFIDACLNKDPSFRPTAKELLKHKFIVKNSKKTSYLTELIDRFKRWKAE 297
                                    27        37        47        57        67        77        87        97       107       117       127       137       147       157        |-       177       187       197       207       217       227       237       247       257       267       277       287       297
                                                                                                                                                                              166        177                                                                                                                        

   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, 2)

Asymmetric Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (36, 36)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (STK26_HUMAN | Q9P289)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0042802    identical protein binding    Interacting selectively and non-covalently with an identical protein or proteins.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    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: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:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    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:0004702    signal transducer, downstream of receptor, with serine/threonine kinase activity    Conveys a signal from an upstream receptor or intracellular signal transducer by catalysis of the reaction: 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:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006921    cellular component disassembly involved in execution phase of apoptosis    The breakdown of structures such as organelles, proteins, or other macromolecular structures during apoptosis.
    GO:0030033    microvillus assembly    Formation of a microvillus, a thin cylindrical membrane-covered projection on the surface of a cell.
    GO:0000278    mitotic cell cycle    Progression through the phases of the mitotic cell cycle, the most common eukaryotic cell cycle, which canonically comprises four successive phases called G1, S, G2, and M and includes replication of the genome and the subsequent segregation of chromosomes into daughter cells. In some variant cell cycles nuclear replication or nuclear division may not be followed by cell division, or G1 and G2 phases may be absent.
    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:0046777    protein autophosphorylation    The phosphorylation by a protein of one or more of its own amino acid residues (cis-autophosphorylation), or residues on an identical protein (trans-autophosphorylation).
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0042981    regulation of apoptotic process    Any process that modulates the occurrence or rate of cell death by apoptotic process.
    GO:0045595    regulation of cell differentiation    Any process that modulates the frequency, rate or extent of cell differentiation, the process in which relatively unspecialized cells acquire specialized structural and functional features.
    GO:1903205    regulation of hydrogen peroxide-induced cell death    Any process that modulates the frequency, rate or extent of hydrogen peroxide-induced cell death.
    GO:0042542    response to hydrogen peroxide    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
    GO:0023014    signal transduction by protein phosphorylation    A process in which the transfer of one or more phosphate groups to a substrate transmits a signal to the phosphorylated substrate.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005798    Golgi-associated vesicle    Any vesicle associated with the Golgi complex and involved in mediating transport within the Golgi or between the Golgi and other parts of the cell.
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0071944    cell periphery    The part of a cell encompassing the cell cortex, the plasma membrane, and any external encapsulating structures.
    GO:0005813    centrosome    A structure comprised of a core structure (in most organisms, a pair of centrioles) and peripheral material from which a microtubule-based structure, such as a spindle apparatus, is organized. Centrosomes occur close to the nucleus during interphase in many eukaryotic cells, though in animal cells it changes continually during the cell-division cycle.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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        STK26_HUMAN | Q9P2893w8i 4fza 4fzd 4fzf 4geh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3GGF)