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(-) Description

Title :  SOLUTION STRUCTURE OF THE FIRST PHORBOL ESTERS/DIACYLGLYCEROL BINDING DOMAIN OF HUMAN PROTEIN KINASE C, DELTA
 
Authors :  H. Abe, K. Miyamoto, N. Tochio, K. Saito, A. Sasagawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  06 Apr 07  (Deposition) - 08 Apr 08  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Metal Binding Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Abe, K. Miyamoto, N. Tochio, K. Saito, A. Sasagawa, S. Koshiba, M. Inoue, T. Kigawa, S. Yokoyama
Solution Structure Of The First Phorbol Esters/Diacylglycerol Binding Domain Of Human Protein Kinase C, Delta
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROTEIN KINASE C DELTA TYPE
    ChainsA
    EC Number2.7.11.13
    EngineeredYES
    Expression System PlasmidP050302-69
    Expression System Vector TypePLASMID
    FragmentPHORBOL ESTERS/DIACYLGLYCEROL BINDING DOMAIN (C1 DOMAIN)
    GenePRKCD
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymNPKC-DELTA

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

NMR Structure (1, 2)
No.NameCountTypeFull Name
1ZN2Ligand/IonZINC ION

(-) Sites  (2, 2)

NMR Structure (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:18 , GLU A:19 , PHE A:20BINDING SITE FOR RESIDUE ZN A 201
2AC2SOFTWARECYS A:31 , CYS A:34BINDING SITE FOR RESIDUE ZN A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2YUU)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ZF_DAG_PE_2PS50081 Zinc finger phorbol-ester/DAG-type profile.KPCD_HUMAN158-208
230-280
  1A:17-67
-
2ZF_DAG_PE_1PS00479 Zinc finger phorbol-ester/DAG-type signature.KPCD_HUMAN159-208
231-280
  1A:18-67
-

(-) Exons   (5, 5)

NMR Structure (5, 5)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.3aENST000003947293aENSE00001905376chr3:53195136-53195444309KPCD_HUMAN-00--
1.7ENST000003947297ENSE00002149439chr3:53212420-53212553134KPCD_HUMAN1-39390--
1.8bENST000003947298bENSE00001079750chr3:53213593-53213792200KPCD_HUMAN39-105670--
1.9ENST000003947299ENSE00002189105chr3:53215223-5321528361KPCD_HUMAN106-126210--
1.10ENST0000039472910ENSE00001079749chr3:53215460-53215622163KPCD_HUMAN126-180551A:1-39 (gaps)52
1.11ENST0000039472911ENSE00001079756chr3:53215717-5321574832KPCD_HUMAN180-191121A:39-5012
1.12ENST0000039472912ENSE00001079752chr3:53217137-5321722286KPCD_HUMAN191-219291A:50-7728
1.13ENST0000039472913ENSE00001079767chr3:53217468-53217597130KPCD_HUMAN220-263440--
1.14bENST0000039472914bENSE00001079762chr3:53218890-53218990101KPCD_HUMAN263-296340--
1.15ENST0000039472915ENSE00001079761chr3:53219620-5321971697KPCD_HUMAN297-329331A:78-814
1.16ENST0000039472916ENSE00001079755chr3:53219943-53220043101KPCD_HUMAN329-362341A:82-832
1.17ENST0000039472917ENSE00001079757chr3:53220183-53220356174KPCD_HUMAN363-420580--
1.18ENST0000039472918ENSE00001079751chr3:53220620-5322071192KPCD_HUMAN421-451310--
1.19ENST0000039472919ENSE00001079754chr3:53221356-5322141863KPCD_HUMAN451-472220--
1.20ENST0000039472920ENSE00001079760chr3:53222736-53222874139KPCD_HUMAN472-518470--
1.21ENST0000039472921ENSE00001079766chr3:53223074-53223262189KPCD_HUMAN519-581630--
1.22ENST0000039472922ENSE00001079764chr3:53223889-53224017129KPCD_HUMAN582-624430--
1.23bENST0000039472923bENSE00001321750chr3:53226124-53226733610KPCD_HUMAN625-676520--

(-) Sequences/Alignments

NMR Structure
   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:83
 aligned with KPCD_HUMAN | Q05655 from UniProtKB/Swiss-Prot  Length:676

    Alignment length:204
                                   138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328    
           KPCD_HUMAN   129 QSMRSEDEAKFPTMNRRGAIKQAKIHYIKNHEFIATFFGQPTFCSVCKDFVWGLNKQGYKCRQCNAAIHKKCIDKIIGRCTGTAANSRDTIFQKERFNIDMPHRFKVHNYMSPTFCDHCGSLLWGLVKQGLKCEDCGMNVHHKCREKVANLCGINQKLLAEALNQVTQRASRRSDSASSEPVGIYQGFEKKTGVAGEDMQDNSG 332
               SCOP domains d2yuua_              A: automated matches                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------C1_1-2yuuA01 A:18-70                                 ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......-------------....eehhhhh.eeee.....................eeee.....ee..hhhhh...............-------------------------------------------------------------------------------------....-----------------------.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                PROSITE (1) -----------------------------ZF_DAG_PE_2  PDB: A:17-67 UniProt: 158-208         ---------------------ZF_DAG_PE_2  PDB: - UniProt: 230-280               ---------------------------------------------------- PROSITE (1)
                PROSITE (2) ------------------------------ZF_DAG_PE_1  PDB: A:18-67 UniProt: 159-208        ----------------------ZF_DAG_PE_1  PDB: - UniProt: 231-280              ---------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.10  PDB: A:1-39 (gaps) UniProt: 126-180      ----------Exon 1.12  PDB: A:50-77      Exon 1.13  PDB: - UniProt: 220-263          ---------------------------------Exon 1.15  PDB: A:78-81          --- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------Exon 1.11   -----------------------------------------------------------------------Exon 1.14b  PDB: -                --------------------------------1.16 Transcript 1 (2)
                 2yuu A   1 GSSGSSG-------------KQAKIHYIKNHEFIATFFGQPTFCSVCKDFVWGLNKQGYKCRQCNAAIHKKCIDKIIGRCTGTAANSRDT-------------------------------------------------------------------------------------SGPS-----------------------SG  83
                                  |  -         -|       17        27        37        47        57        67        77         -         -         -         -         -         -         -         -     |  |-         -         -  | 
                                  7             8                                                                   77                                                                                    78 81                      82 

   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)

NMR Structure

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2YUU)

(-) Pfam Domains  (1, 1)

NMR Structure
(-)
Clan: C1 (13)

(-) Gene Ontology  (80, 80)

NMR Structure(hide GO term definitions)
Chain A   (KPCD_HUMAN | Q05655)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0004699    calcium-independent protein kinase C activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires diacylglycerol but not calcium.
    GO:0008047    enzyme activator activity    Binds to and increases the activity of an enzyme.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0043560    insulin receptor substrate binding    Interacting selectively and non-covalently with any of the insulin receptor substrate (IRS) proteins, adaptor proteins that bind to the transphosphorylated insulin and insulin-like growth factor receptors, are themselves phosphorylated and in turn recruit SH2 domain-containing signaling molecules to form a productive signaling complex.
    GO:0016301    kinase activity    Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
    GO:0019900    kinase binding    Interacting selectively and non-covalently with a kinase, any enzyme that catalyzes the transfer of a phosphate group.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004715    non-membrane spanning protein tyrosine kinase activity    Catalysis of the reaction: ATP + protein L-tyrosine = ADP + protein L-tyrosine phosphate by a non-membrane spanning protein.
    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:0004697    protein kinase C activity    Catalysis of the reaction: ATP + a protein = ADP + a phosphoprotein. This reaction requires diacylglycerol.
    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:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    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:0042100    B cell proliferation    The expansion of a B cell population by cell division. Follows B cell activation.
    GO:0038096    Fc-gamma receptor signaling pathway involved in phagocytosis    An Fc-gamma receptor signaling pathway that contributes to the endocytic engulfment of external particulate material by phagocytes.
    GO:0007202    activation of phospholipase C activity    The initiation of the activity of the inactive enzyme phospolipase C as the result of a series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand.
    GO:0032147    activation of protein kinase activity    Any process that initiates the activity of an inactive protein kinase.
    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:0060326    cell chemotaxis    The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    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:1904385    cellular response to angiotensin    "Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an angiotensin stimulus. Angiotensin is any of three physiologically active peptides (angiotensin II, III, or IV) processed from angiotensinogen."
    GO:0070301    cellular response to hydrogen peroxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
    GO:0071447    cellular response to hydroperoxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydroperoxide stimulus. Hydroperoxides are monosubstitution products of hydrogen peroxide, HOOH.
    GO:0090398    cellular senescence    A cell aging process stimulated in response to cellular stress, whereby normal cells lose the ability to divide through irreversible cell cycle arrest.
    GO:0042742    defense response to bacterium    Reactions triggered in response to the presence of a bacterium that act to protect the cell or organism.
    GO:0016572    histone phosphorylation    The modification of histones by addition of phosphate groups.
    GO:0016064    immunoglobulin mediated immune response    An immune response mediated by immunoglobulins, whether cell-bound or in solution.
    GO:0060333    interferon-gamma-mediated signaling pathway    A series of molecular signals initiated by the binding of interferon-gamma to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription. Interferon gamma is the only member of the type II interferon found so far.
    GO:0032613    interleukin-10 production    The appearance of interleukin-10 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0032615    interleukin-12 production    The appearance of interleukin-12 due to biosynthesis or secretion following a cellular stimulus, resulting in an increase in its intracellular or extracellular levels.
    GO:0035556    intracellular signal transduction    The process in which a signal is passed on to downstream components within the cell, which become activated themselves to further propagate the signal and finally trigger a change in the function or state of the cell.
    GO:0008631    intrinsic apoptotic signaling pathway in response to oxidative stress    A series of molecular signals in which an intracellular signal is conveyed to trigger the apoptotic death of a cell. The pathway is induced in response to oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, and ends when the execution phase of apoptosis is triggered.
    GO:0043407    negative regulation of MAP kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of MAP kinase activity.
    GO:0030837    negative regulation of actin filament polymerization    Any process that stops, prevents, or reduces the frequency, rate or extent of actin polymerization.
    GO:0051490    negative regulation of filopodium assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of the assembly of a filopodium, a thin, stiff protrusion extended by the leading edge of a motile cell such as a crawling fibroblast or amoeba, or an axonal growth cone.
    GO:0034351    negative regulation of glial cell apoptotic process    Any process that stops, prevents, or reduces the frequency, rate, or extent of glial cell apoptotic process.
    GO:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:0046627    negative regulation of insulin receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of insulin receptor signaling.
    GO:0050732    negative regulation of peptidyl-tyrosine phosphorylation    Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
    GO:0090331    negative regulation of platelet aggregation    Any process that decreases the rate, frequency or extent of platelet aggregation. Platelet aggregation is the adhesion of one platelet to one or more other platelets via adhesion molecules.
    GO:0032091    negative regulation of protein binding    Any process that stops, prevents, or reduces the frequency, rate or extent of protein binding.
    GO:0042119    neutrophil activation    The change in morphology and behavior of a neutrophil resulting from exposure to a cytokine, chemokine, cellular ligand, or soluble factor.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    GO:0018107    peptidyl-threonine phosphorylation    The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    GO:0018108    peptidyl-tyrosine phosphorylation    The phosphorylation of peptidyl-tyrosine to form peptidyl-O4'-phospho-L-tyrosine.
    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:0030168    platelet activation    A series of progressive, overlapping events triggered by exposure of the platelets to subendothelial tissue. These events include shape change, adhesiveness, aggregation, and release reactions. When carried through to completion, these events lead to the formation of a stable hemostatic plug.
    GO:2001235    positive regulation of apoptotic signaling pathway    Any process that activates or increases the frequency, rate or extent of apoptotic signaling pathway.
    GO:2000304    positive regulation of ceramide biosynthetic process    Any process that activates or increases the frequency, rate or extent of ceramide biosynthetic process.
    GO:0032079    positive regulation of endodeoxyribonuclease activity    Any process that activates or increases the frequency, rate or extent of endodeoxyribonuclease activity, the hydrolysis of ester linkages within deoxyribonucleic acid by creating internal breaks.
    GO:2000753    positive regulation of glucosylceramide catabolic process    Any process that activates or increases the frequency, rate or extent of glucosylceramide catabolic process.
    GO:1900163    positive regulation of phospholipid scramblase activity    Any process that activates or increases the frequency, rate or extent of phospholipid scramblase activity.
    GO:0035307    positive regulation of protein dephosphorylation    Any process that activates or increases the frequency, rate or extent of removal of phosphate groups from a protein.
    GO:0042307    positive regulation of protein import into nucleus    Any process that activates or increases the frequency, rate or extent of movement of proteins from the cytoplasm into the nucleus.
    GO:2001022    positive regulation of response to DNA damage stimulus    Any process that activates or increases the frequency, rate or extent of response to DNA damage stimulus.
    GO:2000755    positive regulation of sphingomyelin catabolic process    Any process that activates or increases the frequency, rate or extent of sphingomyelin catabolic process.
    GO:0032930    positive regulation of superoxide anion generation    Any process that activates or increases the frequency, rate or extent of enzymatic generation of superoxide by a cell.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0050821    protein stabilization    Any process involved in maintaining the structure and integrity of a protein and preventing it from degradation or aggregation.
    GO:0032956    regulation of actin cytoskeleton organization    Any process that modulates the frequency, rate or extent of the formation, arrangement of constituent parts, or disassembly of cytoskeletal structures comprising actin filaments and their associated proteins.
    GO:0043488    regulation of mRNA stability    Any process that modulates the propensity of mRNA molecules to degradation. Includes processes that both stabilize and destabilize mRNAs.
    GO:0010469    regulation of receptor activity    Any process that modulates the frequency, rate or extent of receptor activity. Receptor activity is when a molecule combines with an extracellular or intracellular messenger to initiate a change in cell activity.
    GO:0007165    signal transduction    The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
    GO:0002223    stimulatory C-type lectin receptor signaling pathway    Any series of molecular signals generated as a consequence of binding to a C-type lectin receptor capable of cellular activation.
    GO:0023021    termination of signal transduction    The signaling process in which signal transduction is brought to an end rather than being reversibly modulated.
cellular component
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    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:0005783    endoplasmic reticulum    The irregular network of unit membranes, visible only by electron microscopy, that occurs in the cytoplasm of many eukaryotic cells. The membranes form a complex meshwork of tubular channels, which are often expanded into slitlike cavities called cisternae. The ER takes two forms, rough (or granular), with ribosomes adhering to the outer surface, and smooth (with no ribosomes attached).
    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:0016363    nuclear matrix    The dense fibrillar network lying on the inner side of the nuclear membrane.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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        KPCD_HUMAN | Q056551yrk

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2YUU)