Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF A PHOSPHORYLATED SMAD2
 
Authors :  J. -W. Wu, M. Hu, J. Chai, J. Seoane, M. Huse, S. Kyin, T. W. Muir, R. Fairma J. Massague, Y. Shi
Date :  01 Dec 01  (Deposition) - 06 Feb 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (3x)
Keywords :  Tgf-Beta Signaling, Smad2, Phosphorylation, Receptor Kinase Signaling, Cancer, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. W. Wu, M. Hu, J. Chai, J. Seoane, M. Huse, C. Li, D. J. Rigotti, S. Kyin, T. W. Muir, R. Fairman, J. Massague, Y. Shi
Crystal Structure Of A Phosphorylated Smad2. Recognition Of Phosphoserine By The Mh2 Domain And Insights On Smad Function In Tgf-Beta Signaling.
Mol. Cell V. 8 1277 2001
PubMed-ID: 11779503  |  Reference-DOI: 10.1016/S1097-2765(01)00421-X

(-) Compounds

Molecule 1 - SMAD2
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1SEP2Mod. Amino AcidPHOSPHOSERINE
Biological Unit 1 (1, 6)
No.NameCountTypeFull Name
1SEP6Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (0, 0)

(no "Site" information available for 1KHX)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (4, 4)

Asymmetric Unit (4, 4)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036473D300VSMAD2_HUMANUnclassified  ---AD300V
2UniProtVAR_011377L440RSMAD2_HUMANUnclassified  ---AL440R
3UniProtVAR_011378P445HSMAD2_HUMANUnclassified  ---AP445H
4UniProtVAR_011379D450ESMAD2_HUMANUnclassified  ---AD450E

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (4, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_036473D300VSMAD2_HUMANUnclassified  ---AD300V
2UniProtVAR_011377L440RSMAD2_HUMANUnclassified  ---AL440R
3UniProtVAR_011378P445HSMAD2_HUMANUnclassified  ---AP445H
4UniProtVAR_011379D450ESMAD2_HUMANUnclassified  ---AD450E

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MH2PS51076 MAD homology domain 2 (MH2) profile.SMAD2_HUMAN274-467  1A:274-467
Biological Unit 1 (1, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1MH2PS51076 MAD homology domain 2 (MH2) profile.SMAD2_HUMAN274-467  3A:274-467

(-) Exons   (4, 4)

Asymmetric Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENST000002621602ENSE00001533831chr18:45456930-45456732199SMAD2_HUMAN-00--
1.3ENST000002621603ENSE00001191187chr18:45423180-45422892289SMAD2_HUMAN1-79790--
1.4ENST000002621604ENSE00001248514chr18:45396935-4539684690SMAD2_HUMAN79-109310--
1.5ENST000002621605ENSE00001248509chr18:45395807-45395614194SMAD2_HUMAN109-174660--
1.6ENST000002621606ENSE00001248503chr18:45394828-45394694135SMAD2_HUMAN174-219460--
1.7ENST000002621607ENSE00001728507chr18:45391504-4539143075SMAD2_HUMAN219-244260--
1.8ENST000002621608ENSE00001248493chr18:45377698-4537764554SMAD2_HUMAN244-262190--
1.9ENST000002621609ENSE00001248484chr18:45375058-45374846213SMAD2_HUMAN262-333721A:265-33369
1.10ENST0000026216010ENSE00001248481chr18:45372171-45372034138SMAD2_HUMAN333-379471A:333-37947
1.11ENST0000026216011ENSE00001598119chr18:45371855-45371711145SMAD2_HUMAN379-427491A:379-42749
1.12bENST0000026216012bENSE00001949705chr18:45368321-4535792210400SMAD2_HUMAN427-467411A:427-46741

(-) 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:203
 aligned with SMAD2_HUMAN | Q15796 from UniProtKB/Swiss-Prot  Length:467

    Alignment length:203
                                   274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464   
          SMAD2_HUMAN   265 PVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNSERFCLGLLSNVNRNATVEMTRRHIGRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEFAALLAQSVNQGFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSSMS 467
               SCOP domains d1khxa_ A: Smad2 MH2 domain                                                                                                                                                                                 SCOP domains
               CATH domains 1khxA00 A:265-466  [code=2.60.200.10, no name defined]                                                                                                                                                    - CATH domains
               Pfam domains ---MH2-1khxA01 A:268-445                                                                                                                                                             ---------------------- Pfam domains
         Sec.struct. author ..........eeeeeee..ee....eee...eeeee.........eee.hhh.....hhhhhhhhh.....eeeeee..eeeeee.....eeeehhhhhhhh.......eee....eeeeeehhhhhhhhhhhh..hhhhhhhhhhh.eeeeee...........hhhhh..eeeeeehhhhhhhhhhhh............. Sec.struct. author
                 SAPs(SNPs) -----------------------------------V-------------------------------------------------------------------------------------------------------------------------------------------R----H----E----------------- SAPs(SNPs)
                    PROSITE ---------MH2  PDB: A:274-467 UniProt: 274-467                                                                                                                                                               PROSITE
           Transcript 1 (1) --------------------------------------------------------------------Exon 1.10  PDB: A:333-379 UniProt: 333-379     -----------------------------------------------Exon 1.12b  PDB: A:427-467                Transcript 1 (1)
           Transcript 1 (2) Exon 1.9  PDB: A:265-333 UniProt: 262-333 [INCOMPLETE]               ---------------------------------------------Exon 1.11  PDB: A:379-427 UniProt: 379-427       ---------------------------------------- Transcript 1 (2)
                 1khx A 265 PVTYSEPAFWCSIAYYELNQRVGETFHASQPSLTVDGFTDPSNSERFCLGLLSNVNRNATVEMTRRHIGRGVRLYYIGGEVFAECLSDSAIFVQSPNCNQRYGWHPATVCKIPPGCNLKIFNNQEFAALLAQSVNQGFEAVYQLTRMCTIRMSFVKGWGAEYRRQTVTSTPCWIELHLNGPLQWLDKVLTQMGSPSVRCSsMs 467
                                   274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464| |
                                                                                                                                                                                                                                  465-SEP
                                                                                                                                                                                                                                    467-SEP

   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  (1, 1)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (1, 1)

Asymmetric Unit
(-)
Clan: SMAD-FHA (27)

(-) Gene Ontology  (85, 85)

Asymmetric Unit(hide GO term definitions)
Chain A   (SMAD2_HUMAN | Q15796)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0070411    I-SMAD binding    Interacting selectively and non-covalently with an inhibitory SMAD signaling protein.
    GO:0070412    R-SMAD binding    Interacting selectively and non-covalently with a receptor-regulated SMAD signaling protein.
    GO:0000978    RNA polymerase II core promoter proximal region sequence-specific DNA binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II.
    GO:0046332    SMAD binding    Interacting selectively and non-covalently with a SMAD signaling protein.
    GO:0033613    activating transcription factor binding    Interacting selectively and non-covalently with an activating transcription factor, any protein whose activity is required to initiate or upregulate transcription.
    GO:0003682    chromatin binding    Interacting selectively and non-covalently with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0070410    co-SMAD binding    Interacting selectively and non-covalently with a common mediator SMAD signaling protein.
    GO:0003690    double-stranded DNA binding    Interacting selectively and non-covalently with double-stranded DNA.
    GO:0035326    enhancer binding    Interacting selectively and non-covalently with an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0019902    phosphatase binding    Interacting selectively and non-covalently with any phosphatase.
    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:0046982    protein heterodimerization activity    Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0003700    transcription factor activity, sequence-specific DNA binding    Interacting selectively and non-covalently with a specific DNA sequence in order to modulate transcription. The transcription factor may or may not also interact selectively with a protein or macromolecular complex.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0001077    transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in cis with and relatively close to a core promoter for RNA polymerase II (RNAP II) in order to activate or increase the frequency, rate or extent of transcription from the RNAP II promoter.
    GO:0005160    transforming growth factor beta receptor binding    Interacting selectively and non-covalently with the transforming growth factor beta receptor.
    GO:0030618    transforming growth factor beta receptor, pathway-specific cytoplasmic mediator activity    A TGF-beta cytoplasmic mediator that is phosphorylated by a TGFbeta receptor and complexes with a common-partner mediator. The- heterocomplex translocates to the nucleus to regulate transcription.
    GO:0034713    type I transforming growth factor beta receptor binding    Interacting selectively and non-covalently with a type I transforming growth factor beta receptor.
    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:0007183    SMAD protein complex assembly    The aggregation, arrangement and bonding together of a set of components to form a protein complex that contains SMAD proteins.
    GO:0060395    SMAD protein signal transduction    The cascade of processes by which a signal interacts with a receptor, causing a change in the activity of a SMAD protein, and ultimately effecting a change in the functioning of the cell.
    GO:0032924    activin receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to an activin receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0009952    anterior/posterior pattern specification    The regionalization process in which specific areas of cell differentiation are determined along the anterior-posterior axis. The anterior-posterior axis is defined by a line that runs from the head or mouth of an organism to the tail or opposite end of the organism.
    GO:0045165    cell fate commitment    The commitment of cells to specific cell fates and their capacity to differentiate into particular kinds of cells. Positional information is established through protein signals that emanate from a localized source within a cell (the initial one-cell zygote) or within a developmental field.
    GO:0007182    common-partner SMAD protein phosphorylation    The process of introducing a phosphate group on to a common-partner SMAD protein. A common partner SMAD protein binds to pathway-restricted SMAD proteins forming a complex that translocates to the nucleus.
    GO:0048589    developmental growth    The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
    GO:0048701    embryonic cranial skeleton morphogenesis    The process in which the anatomical structures of the cranial skeleton are generated and organized during the embryonic phase.
    GO:0048617    embryonic foregut morphogenesis    The process in which the anatomical structures of the foregut are generated and organized, during the embryonic phase.
    GO:0009880    embryonic pattern specification    The process that results in the patterns of cell differentiation that will arise in an embryo.
    GO:0007492    endoderm development    The process whose specific outcome is the progression of the endoderm over time, from its formation to the mature structure. The endoderm is the innermost germ layer that develops into the gastrointestinal tract, the lungs and associated tissues.
    GO:0001706    endoderm formation    The formation of the endoderm during gastrulation.
    GO:0007369    gastrulation    A complex and coordinated series of cellular movements that occurs at the end of cleavage during embryonic development of most animals. The details of gastrulation vary from species to species, but usually result in the formation of the three primary germ layers, ectoderm, mesoderm and endoderm.
    GO:0007507    heart development    The process whose specific outcome is the progression of the heart over time, from its formation to the mature structure. The heart is a hollow, muscular organ, which, by contracting rhythmically, keeps up the circulation of the blood.
    GO:0001701    in utero embryonic development    The process whose specific outcome is the progression of the embryo in the uterus over time, from formation of the zygote in the oviduct, to birth. An example of this process is found in Mus musculus.
    GO:0030073    insulin secretion    The regulated release of proinsulin from secretory granules (B granules) in the B cells of the pancreas; accompanied by cleavage of proinsulin to form mature insulin.
    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:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0001707    mesoderm formation    The process that gives rise to the mesoderm. This process pertains to the initial formation of the structure from unspecified parts.
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    GO:0010629    negative regulation of gene expression    Any process that decreases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0000122    negative regulation of transcription from RNA polymerase II promoter    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045892    negative regulation of transcription, DNA-templated    Any process that stops, prevents, or reduces the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0030512    negative regulation of transforming growth factor beta receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.
    GO:0038092    nodal signaling pathway    A series of molecular signals initiated by the binding of a nodal protein to an activin receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0035265    organ growth    The increase in size or mass of an organ. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that function together as to perform a specific function.
    GO:0060021    palate development    The biological process whose specific outcome is the progression of the palate from an initial condition to its mature state. This process begins with the formation of the structure and ends with the mature structure. The palate is the partition that separates the nasal and oral cavities.
    GO:0031016    pancreas development    The process whose specific outcome is the progression of the pancreas over time, from its formation to the mature structure. The pancreas is an endoderm derived structure that produces precursors of digestive enzymes and blood glucose regulating enzymes.
    GO:0048340    paraxial mesoderm morphogenesis    The process in which the anatomical structures of the paraxial mesoderm are generated and organized.
    GO:0007389    pattern specification process    Any developmental process that results in the creation of defined areas or spaces within an organism to which cells respond and eventually are instructed to differentiate.
    GO:0060039    pericardium development    The process whose specific outcome is the progression of the pericardium over time, from its formation to the mature structure. The pericardium is a double-walled sac that contains the heart and the roots of the aorta, vena cava and the pulmonary artery.
    GO:0030513    positive regulation of BMP signaling pathway    Any process that activates or increases the frequency, rate or extent of BMP signaling pathway activity.
    GO:0010718    positive regulation of epithelial to mesenchymal transition    Any process that increases the rate, frequency, or extent of epithelial to mesenchymal transition. Epithelial to mesenchymal transition is where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:1900224    positive regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry    Any process that activates or increases the frequency, rate or extent of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0045893    positive regulation of transcription, DNA-templated    Any process that activates or increases the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    GO:0031053    primary miRNA processing    Any process involved in the conversion of a primary microRNA transcript into a pre-microRNA molecule.
    GO:0006468    protein phosphorylation    The process of introducing a phosphate group on to a protein.
    GO:0051098    regulation of binding    Any process that modulates the frequency, rate or extent of binding, the selective interaction of a molecule with one or more specific sites on another molecule.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0017015    regulation of transforming growth factor beta receptor signaling pathway    Any process that modulates the frequency, rate or extent of activity of any TGF-beta receptor signaling pathway.
    GO:0070723    response to cholesterol    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 cholesterol stimulus.
    GO:0009749    response to glucose    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 glucose stimulus.
    GO:0023019    signal transduction involved in regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression as a consequence of a process in which a signal is released and/or conveyed from one location to another.
    GO:0035019    somatic stem cell population maintenance    Any process by which an organism retains a population of somatic stem cells, undifferentiated cells in the embryo or adult which can undergo unlimited division and give rise to cell types of the body other than those of the germ-line.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0007179    transforming growth factor beta receptor signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to a transforming growth factor beta receptor on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0001657    ureteric bud development    The process whose specific outcome is the progression of the ureteric bud over time, from its formation to the mature structure.
    GO:0007352    zygotic specification of dorsal/ventral axis    The specification of the dorsal/ventral axis of the embryo, through the products of genes expressed in the zygote.
cellular component
    GO:0071141    SMAD protein complex    A protein complex that consists of only SMAD proteins; may be homomeric or heteromeric.
    GO:0071144    SMAD2-SMAD3 protein complex    A heteromeric SMAD protein complex that contains SMAD2 and SMAD3.
    GO:0032444    activin responsive factor complex    A transcriptionally active complex that binds to an activin response element (ARE) in the promoter of target genes, and is composed of two SMAD2 proteins, one SMAD4 protein and a Forkhead activin signal transducer (FAST) transcription factor.
    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:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0000790    nuclear chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome in the nucleus.
    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:0043234    protein complex    A stable macromolecular complex composed (only) of two or more polypeptide subunits along with any covalently attached molecules (such as lipid anchors or oligosaccharide) or non-protein prosthetic groups (such as nucleotides or metal ions). Prosthetic group in this context refers to a tightly bound cofactor. The component polypeptide subunits may be identical.
    GO:0005667    transcription factor complex    A protein complex that is capable of associating with DNA by direct binding, or via other DNA-binding proteins or complexes, and regulating transcription.

 Visualization

(-) Interactive Views

Asymmetric 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)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(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
    SEP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 1khx)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1khx)
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

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

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1khx
    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
  SMAD2_HUMAN | Q15796
    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
  SMAD2_HUMAN | Q15796
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        SMAD2_HUMAN | Q157961dev 1u7v 2lb3

(-) Related Entries Specified in the PDB File

1dev