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(-) Description

Title :  SOLUTION STRUCTURE OF RSGI RUH-028, A HOMEOBOX DOMAIN FROM HUMAN CDNA
 
Authors :  A. Nakamura, S. Ohnishi, T. Abe, N. Nameki, N. Tochio, S. Koshiba, T. Kigawa, S. Yokoyama, S. Kawaii, H. Hirota, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date :  27 Oct 06  (Deposition) - 14 Nov 06  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A  (20x)
Keywords :  Dna Binding Protein, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Nakamura, S. Ohnishi, T. Abe, N. Nameki, N. Tochio, S. Koshiba, T. Kigawa, S. Yokoyama, S. Kawaii, H. Hirota
Solution Structure Of Rsgi Ruh-028, A Homeobox Domain From Human Cdna
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HOMEOBOX PROTEIN PRH
    ChainsA
    EngineeredYES
    Expression SystemCELL FREE SYNTHESIS
    Expression System PlasmidP040315-39
    Expression System Vector TypePLASMID
    FragmentHOMEOBOX DOMAIN
    GeneHHEX, HEX, PRH, PRHX
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Other DetailsCELL-FREE PROTEIN SYNTHESIS
    SynonymHEMATOPOIETICALLY EXPRESSED HOMEOBOX, HOMEOBOX PROTEIN HEX

 Structural Features

(-) Chains, Units

  
NMR Structure (20x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 2E1O)

(-) Sites  (0, 0)

(no "Site" information available for 2E1O)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2E1O)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2E1O)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2E1O)

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_2PS50071 'Homeobox' domain profile.HHEX_HUMAN135-195  1A:8-64
2HOMEOBOX_1PS00027 'Homeobox' domain signature.HHEX_HUMAN170-193  1A:40-63

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002827281ENSE00001007290chr10:94449712-94450104393HHEX_HUMAN1-1211211A:1-77
1.2cENST000002827282cENSE00001007293chr10:94452125-94452303179HHEX_HUMAN121-180601A:8-5043
1.3ENST000002827283ENSE00001007291chr10:94452459-9445250951HHEX_HUMAN181-197171A:51-6515
1.4cENST000002827284cENSE00001162575chr10:94454304-944553971094HHEX_HUMAN198-270731A:66-705

(-) 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:70
 aligned with HHEX_HUMAN | Q03014 from UniProtKB/Swiss-Prot  Length:270

    Alignment length:112
                                   101       111       121       131       141       151       161       171       181       191       201  
           HHEX_HUMAN    92 GPGGFGGPLYPFPRTVNDYTHALLRHDPLGKPLLWSPFLQRPLHKRKGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRLKQENPQSN 203
               SCOP domains ----------------------------------------------d2e1oa1 A:8-64 Homeobox protein prh                      --------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......---------------------------------------.......hhhhhhhhhhhhhhh...hhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh---h.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------HOMEOBOX_2  PDB: A:8-64 UniProt: 135-195                     -------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------HOMEOBOX_1  PDB: A:40-63---------- PROSITE (2)
           Transcript 1 (1) Exon 1.1  PDB: A:1-7          -----------------------------------------------------------Exon 1.3         1.4c   Transcript 1 (1)
           Transcript 1 (2) -----------------------------Exon 1.2c  PDB: A:8-50 UniProt: 121-180 [INCOMPLETE]        ----------------------- Transcript 1 (2)
                 2e1o A   1 GSSGSSG---------------------------------------KGGQVRFSNDQTIELEKKFETQKYLSPPERKRLAKMLQLSERQVKTWFQNRRAKWRRS---GPSSG  70
                                  |  -         -         -         -      | 11        21        31        41        51        61   |   |68  
                                  7                                       8                                                       65  66    

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    → 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 2E1O)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2E1O)

(-) Gene Ontology  (69, 69)

NMR Structure(hide GO term definitions)
Chain A   (HHEX_HUMAN | Q03014)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0008301    DNA binding, bending    The activity of binding selectively and non-covalently to and distorting the original structure of DNA, typically a straight helix, into a bend, or increasing the bend if the original structure was intrinsically bent due to its sequence.
    GO:0071837    HMG box domain binding    Interacting selectively and non-covalently with an HMG box domain, a protein domain that consists of three helices in an irregular array. HMG-box domains are found in one or more copies in HMG-box proteins, which form a large, diverse family involved in the regulation of DNA-dependent processes such as transcription, replication, and strand repair, all of which require the bending and unwinding of chromatin.
    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:0000977    RNA polymerase II regulatory region sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of a regulatory region that controls the transcription of a gene or cistron by RNA polymerase II.
    GO:0017025    TBP-class protein binding    Interacting selectively and non-covalently with a member of the class of TATA-binding proteins (TBP), including any of the TBP-related factors (TRFs).
    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:0008190    eukaryotic initiation factor 4E binding    Interacting selectively and non-covalently with eukaryotic initiation factor 4E, a polypeptide factor involved in the initiation of ribosome-mediated translation.
    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:0070491    repressing transcription factor binding    Interacting selectively and non-covalently with a transcription repressor, any protein whose activity is required to prevent or downregulate transcription.
    GO:0043565    sequence-specific DNA binding    Interacting selectively and non-covalently with DNA of a specific nucleotide composition, e.g. GC-rich DNA binding, or with a specific sequence motif or type of DNA e.g. promotor binding or rDNA binding.
    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:0044212    transcription regulatory region DNA binding    Interacting selectively and non-covalently with a DNA region that regulates the transcription of a region of DNA, which may be a gene, cistron, or operon. Binding may occur as a sequence specific interaction or as an interaction observed only once a factor has been recruited to the DNA by other factors.
    GO:0001078    transcriptional repressor 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 stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0001227    transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding    Interacting selectively and non-covalently with a sequence of DNA that is in the regulatory region for RNA polymerase II (RNAP II) in order to stop, prevent, or reduce the frequency, rate or extent of transcription from an RNA polymerase II promoter.
biological process
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0071103    DNA conformation change    A cellular process that results in a change in the spatial configuration of a DNA molecule. A conformation change can bend DNA, or alter the, twist, writhe, or linking number of a DNA molecule.
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    GO:0009887    animal organ morphogenesis    Morphogenesis of an animal organ. An organ is defined as a tissue or set of tissues that work together to perform a specific function or functions. Morphogenesis is the process in which anatomical structures are generated and organized. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    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:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0061009    common bile duct development    The progression of the common bile duct over time, from its formation to the mature structure. The common bile duct is formed from the joining of the common hepatic duct running from the liver, and the cystic duct running from the gall bladder. The common bile duct transports bile from the liver and gall bladder to the intestine.
    GO:0035050    embryonic heart tube development    The process whose specific outcome is the progression of the embryonic heart tube over time, from its formation to the mature structure. The heart tube forms as the heart rudiment from the heart field.
    GO:0048568    embryonic organ development    Development, taking place during the embryonic phase, of a tissue or tissues that work together to perform a specific function or functions. Development pertains to the process whose specific outcome is the progression of a structure over time, from its formation to the mature structure. Organs are commonly observed as visibly distinct structures, but may also exist as loosely associated clusters of cells that work together to perform a specific function or functions.
    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:0030900    forebrain development    The process whose specific outcome is the progression of the forebrain over time, from its formation to the mature structure. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0048853    forebrain morphogenesis    The process in which the anatomical structures of the forebrain are generated and organized. The forebrain is the anterior of the three primary divisions of the developing chordate brain or the corresponding part of the adult brain (in vertebrates, includes especially the cerebral hemispheres, the thalamus, and the hypothalamus and especially in higher vertebrates is the main control center for sensory and associative information processing, visceral functions, and voluntary motor functions).
    GO:0061010    gall bladder development    The progression of the gall bladder over time, from its initial formation to the mature structure. The gall bladder is a cavitated organ that stores bile.
    GO:0030097    hemopoiesis    The process whose specific outcome is the progression of the myeloid and lymphoid derived organ/tissue systems of the blood and other parts of the body over time, from formation to the mature structure. The site of hemopoiesis is variable during development, but occurs primarily in bone marrow or kidney in many adult vertebrates.
    GO:0061011    hepatic duct development    The progression of the hepatic duct over time, from its formation to the mature structure. The hepatic duct is the duct that leads from the liver to the common bile duct.
    GO:0061017    hepatoblast differentiation    The process in which a relatively unspecialized cell acquires specialized features of a hepatoblast. A hepatoblast is a cell that retains the ability to divide and proliferate throughout life to provide progenitor cells that can differentiate into hepatocytes and cholangiocytes.
    GO:0070365    hepatocyte differentiation    The process in which a relatively unspecialized cell acquires the specialized features of a hepatocyte. A hepatocyte is specialized epithelial cell that is organized into interconnected plates called lobules, and is the main structural component of the liver.
    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:0022027    interkinetic nuclear migration    The movement of the nucleus of the ventricular zone cell between the apical and the basal zone surfaces. Mitosis occurs when the nucleus is near the apical surface, that is, the lumen of the ventricle.
    GO:0001889    liver development    The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
    GO:0006406    mRNA export from nucleus    The directed movement of mRNA from the nucleus to the cytoplasm.
    GO:0002009    morphogenesis of an epithelium    The process in which the anatomical structures of epithelia are generated and organized. An epithelium consists of closely packed cells arranged in one or more layers, that covers the outer surfaces of the body or lines any internal cavity or tube.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0035264    multicellular organism growth    The increase in size or mass of an entire multicellular organism, as opposed to cell growth.
    GO:0002573    myeloid leukocyte differentiation    The process in which a relatively unspecialized myeloid precursor cell acquires the specialized features of any cell of the myeloid leukocyte lineage.
    GO:0016525    negative regulation of angiogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
    GO:0045736    negative regulation of cyclin-dependent protein serine/threonine kinase activity    Any process that stops, prevents, or reduces the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
    GO:0010944    negative regulation of transcription by competitive promoter binding    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves direct competition for interaction with a promoter binding site.
    GO:0010621    negative regulation of transcription by transcription factor localization    Any process that stops, prevents, or reduces the frequency, rate or extent of DNA-dependent transcription using a mechanism that involves the localization of a transcription factor.
    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:0030948    negative regulation of vascular endothelial growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of vascular endothelial growth factor receptor signaling pathway activity.
    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:0016973    poly(A)+ mRNA export from nucleus    The directed movement of poly(A)+ mRNA out of the nucleus into the cytoplasm.
    GO:0030177    positive regulation of Wnt signaling pathway    Any process that activates or increases the frequency, rate or extent of Wnt signal transduction.
    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:0060431    primary lung bud formation    The morphogenetic process in which the foregut region specified to become the lung forms the initial left and right buds.
    GO:0090009    primitive streak formation    The developmental process pertaining to the initial formation of the primitive streak from unspecified parts. The primitive streak is a ridge of cells running along the midline of the embryo where the mesoderm ingresses. It defines the anterior-posterior axis.
    GO:0034504    protein localization to nucleus    A process in which a protein transports or maintains the localization of another protein to the nucleus.
    GO:0042127    regulation of cell proliferation    Any process that modulates the frequency, rate or extent of cell proliferation.
    GO:0006357    regulation of transcription from RNA polymerase II promoter    Any process that modulates the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    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:0030878    thyroid gland development    The process whose specific outcome is the progression of the thyroid gland over time, from its formation to the mature structure. The thyroid gland is an endoderm-derived gland that produces thyroid hormone.
    GO:0048729    tissue morphogenesis    The process in which the anatomical structures of a tissue are generated and organized.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0001570    vasculogenesis    The differentiation of endothelial cells from progenitor cells during blood vessel development, and the de novo formation of blood vessels and tubes.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0032993    protein-DNA complex    A macromolecular complex containing both protein and DNA molecules.

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