Show PDB file:   
         Plain Text   HTML   (compressed file size)
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Authors :  T. C. Diller, N. H. Xuong, S. S. Taylor
Date :  28 Aug 99  (Deposition) - 07 Mar 01  (Release) - 24 Feb 09  (Revision)
Resolution :  2.45
Chains :  Asym./Biol. Unit :  A
Keywords :  Beta Barrel, Camp-Dependent Protein Kinase, Camp-Binding, Regulatory Subunit, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  T. C. Diller, Madhusudan, N. H. Xuong, S. S. Taylor
Molecular Basis For Regulatory Subunit Diversity In Camp-Dependent Protein Kinase: Crystal Structure Of The Type Ii Beta Regulatory Subunit.
Structure V. 9 73 2001
PubMed-ID: 11342137  |  Reference-DOI: 10.1016/S0969-2126(00)00556-6
(for further references see the PDB file header)

(-) Compounds

    Expression SystemESCHERICHIA COLI
    Expression System PlasmidINVITROGEN PRSET B
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism CommonNORWAY RAT
    Organism ScientificRATTUS NORVEGICUS
    Organism Taxid10116

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
1AC1SOFTWARETYR A:213 , PHE A:219 , GLY A:220 , GLU A:221 , LEU A:222 , ALA A:223 , ARG A:230 , ALA A:231 , ALA A:232 , ILE A:234 , ARG A:381 , HOH A:509 , HOH A:522 , HOH A:628BINDING SITE FOR RESIDUE CMP A 440
2AC2SOFTWAREILE A:321 , ILE A:339 , PHE A:348 , GLY A:349 , GLU A:350 , LEU A:351 , ALA A:352 , ARG A:359 , ALA A:360 , ALA A:361 , TYR A:397 , GLN A:400 , HOH A:510 , HOH A:512BINDING SITE FOR RESIDUE CMP A 450

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1CX4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1CX4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1CX4)

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
1CNMP_BINDING_3PS50042 cAMP/cGMP binding motif profile.KAP3_RAT152-271
2CNMP_BINDING_1PS00888 Cyclic nucleotide-binding domain signature 1.KAP3_RAT179-195
3CNMP_BINDING_2PS00889 Cyclic nucleotide-binding domain signature 2.KAP3_RAT219-236

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) 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:275
 aligned with KAP3_RAT | P12369 from UniProtKB/Swiss-Prot  Length:416

    Alignment length:283
                                   139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409   
               SCOP domains d1cx4a1 A:130-265 Regulatory subunit of Protein kinase A                                                                                d1cx4a2 A:266-412 Regulatory subunit of Protein kinase A                                                                                            SCOP domains
               CATH domains 1cx4A01 A:130-255 Jelly Rolls                                                                                                 1cx4A02 A:256-407 Jelly Rolls                                                                                                                           ----- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ----------------------CNMP_BINDING_3  PDB: A:152-271 UniProt: 152-271                                                                         --CNMP_BINDING_3  PDB: A:274-400 UniProt: 274-400                                                                                ------------ PROSITE (1)
                PROSITE (2) -------------------------------------------------CNMP_BINDING_1   -----------------------CNMP_BINDING_2    ----------------------------------------------------------------CNMP_BINDING_1   ------------------------------CNMP_BINDING_2    ----------------------------------------------- PROSITE (2)
           Transcript 1 (1) 1Exon 1.5  PDB: A:131-158    Exon 1.6  PDB: A:159-194            ---------------------------------------------------Exon 1.8  PDB: A:246-279          Exon 1.9  PDB: A:280-304 Exon 1.10 [INCOMPLETE]Exon 1.11  PDB: A:334-373 UniProt: 327-373     --------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------------Exon 1.7  PDB: A:194-245 UniProt: 194-245           -------------------------------------------------------------------------------------------------------------------------------Exon 1.12b  PDB: A:373-412 [INCOMPLETE]  Transcript 1 (2)
                                   139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319     |   -    |  339       349       359       369       379       389       399       409   
                                                                                                                                                                                                                             325      334                                                                              

   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/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1CX4)

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (KAP3_RAT | P12369)
molecular function
    GO:0030552    cAMP binding    Interacting selectively and non-covalently with cAMP, the nucleotide cyclic AMP (adenosine 3',5'-cyclophosphate).
    GO:0004862    cAMP-dependent protein kinase inhibitor activity    Stops, prevents or reduces the activity of a cAMP-dependent protein kinase.
    GO:0008603    cAMP-dependent protein kinase regulator activity    Modulation of the activity of the enzyme cAMP-dependent protein kinase.
    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:0019904    protein domain specific binding    Interacting selectively and non-covalently with a specific domain of a protein.
    GO:0034236    protein kinase A catalytic subunit binding    Interacting selectively and non-covalently with one or both of the catalytic subunits of protein kinase A.
    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:0031625    ubiquitin protein ligase binding    Interacting selectively and non-covalently with a ubiquitin protein ligase enzyme, any of the E3 proteins.
biological process
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    GO:0007612    learning    Any process in an organism in which a relatively long-lasting adaptive behavioral change occurs as the result of experience.
    GO:2000480    negative regulation of cAMP-dependent protein kinase activity    Any process that stops, prevents or reduces the frequency, rate or extent of cAMP-dependent protein kinase activity.
    GO:0045859    regulation of protein kinase activity    Any process that modulates the frequency, rate or extent of protein kinase activity.
    GO:0001932    regulation of protein phosphorylation    Any process that modulates the frequency, rate or extent of addition of phosphate groups into an amino acid in a protein.
    GO:0097332    response to antipsychotic drug    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 an antipsychotic drug stimulus. Antipsychotic drugs are agents that control agitated psychotic behaviour, alleviate acute psychotic states, reduce psychotic symptoms, and exert a quieting effect.
    GO:0097338    response to clozapine    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 clozapine stimulus.
cellular component
    GO:0005952    cAMP-dependent protein kinase complex    An enzyme complex, composed of regulatory and catalytic subunits, that catalyzes protein phosphorylation. Inactive forms of the enzyme have two regulatory chains and two catalytic chains; activation by cAMP produces two active catalytic monomers and a regulatory dimer.
    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:0097546    ciliary base    Area of the cilium (also called flagellum) where the basal body and the axoneme are anchored to the plasma membrane. The ciliary base encompasses the distal part of the basal body, transition fibers and transition zone and is structurally and functionally very distinct from the rest of the cilium. In this area proteins are sorted and filtered before entering the cilium, and many ciliary proteins localize specifically to this area.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    GO:0043198    dendritic shaft    Cylindric portion of the dendrite, directly stemming from the perikaryon, and carrying the dendritic spines.
    GO:0043197    dendritic spine    A small, membranous protrusion from a dendrite that forms a postsynaptic compartment - typically receiving input from a single presynapse. They function as partially isolated biochemical and an electrical compartments. Spine morphology is variable including "thin", "stubby", "mushroom", and "branched", with a continuum of intermediate morphologies. They typically terminate in a bulb shape, linked to the dendritic shaft by a restriction. Spine remodeling is though to be involved in synaptic plasticity.
    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:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    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.


(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
  Ligands, Modified Residues, Ions
    CMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1cx4)

(-) Still Images

  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
Access by UniProt ID/Accession number
  KAP3_RAT | P12369
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
Access by UniProt ID/Accession number
  KAP3_RAT | P12369
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

        KAP3_RAT | P123693idb 3idc 4jva

(-) Related Entries Specified in the PDB File