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(-) Description

Title :  PHAGE-SELECTED HOMEODOMAIN BOUND TO UNMODIFIED DNA
 
Authors :  K. M. Shokat, M. E. Feldman, M. D. Simon
Date :  16 Jul 06  (Deposition) - 12 Dec 06  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Homeodomain, Phage Display, Transcription-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. D. Simon, M. E. Feldman, D. Rauh, A. E. Maris, D. E. Wemmer, K. M. Shoka
Structure And Properties Of A Re-Engineered Homeodomain Protein-Dna Interface.
Acs Chem. Biol. V. 1 755 2006
PubMed-ID: 17240973  |  Reference-DOI: 10.1021/CB6003756

(-) Compounds

Molecule 1 - 5'-D(*TP*TP*TP*TP*GP*CP*CP*AP*TP*GP*TP*AP*AP*TP*CP*CP*CP*CP *GP*GP*A)-3'
    ChainsC
    EngineeredYES
    Other DetailsCOMMERCIAL SOLID PHASE SYNTHESIS
    SyntheticYES
 
Molecule 2 - 5'-D(*AP*TP*CP*CP*GP*GP*GP*GP*AP*TP*TP*AP*CP*AP*TP*GP*GP*CP *AP*AP*A)-3'
    ChainsD
    EngineeredYES
    Other DetailsCOMMERCIAL SOLID PHASE SYNTHESIS
    SyntheticYES
 
Molecule 3 - SEGMENTATION POLARITY HOMEOBOX PROTEIN ENGRAILED
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPMAL-ENHDF
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePMAL-C2
    FragmentENGRAILED HOMEODOMAIN
    GeneEN
    MutationYES
    Organism CommonFRUIT FLY
    Organism ScientificDROSOPHILA MELANOGASTER
    Organism Taxid7227
    SynonymHOMEOBOX

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 5)

Asymmetric/Biological Unit (2, 5)
No.NameCountTypeFull Name
13MO1Ligand/Ion3-METHYL-1,3-OXAZOLIDIN-2-ONE
2GOL4Ligand/IonGLYCEROL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER B:9 , GLU B:11 , TYR B:25 , LEU B:38 , GOL C:204BINDING SITE FOR RESIDUE 3MO B 301
2AC2SOFTWAREASN A:51 , MET A:52 , LYS A:55 , HOH A:206 , HOH A:209 , DT C:11 , DA C:12BINDING SITE FOR RESIDUE GOL A 201
3AC3SOFTWAREPHE B:20 , ASN B:21 , ARG B:24 , HOH B:308BINDING SITE FOR RESIDUE GOL B 202
4AC4SOFTWAREARG B:24 , TYR B:25 , GLU B:37 , ARG B:53 , HOH C:210BINDING SITE FOR RESIDUE GOL B 203
5AC5SOFTWARE3MO B:301 , DC C:18 , DG C:19 , HOH C:227BINDING SITE FOR RESIDUE GOL C 204

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 2)

Asymmetric/Biological Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1HOMEOBOX_1PS00027 'Homeobox' domain signature.HMEN_DROME487-510
 
  2A:34-57
B:34-57

(-) Exons   (0, 0)

(no "Exon" information available for 2HOS)

(-) 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:56
 aligned with HMEN_DROME | P02836 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:56
                                   467       477       487       497       507      
           HMEN_DROME   458 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKST 513
               SCOP domains d2hosa_ A: Engrailed Homeodomain                         SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------HOMEOBOX_1  PDB: A:34-57--- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                 2hos A   5 RTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKKST  60
                                    14        24        34        44        54      

Chain B from PDB  Type:PROTEIN  Length:58
 aligned with HMEN_DROME | P02836 from UniProtKB/Swiss-Prot  Length:552

    Alignment length:58
                                   464       474       484       494       504        
           HMEN_DROME   455 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQIKIWFQNKRAKIKKS 512
               SCOP domains d2hosb_ B: Engrailed Homeodomain                           SCOP domains
               CATH domains ---------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh...hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------HOMEOBOX_1  PDB: B:34-57-- PROSITE
                 Transcript ---------------------------------------------------------- Transcript
                 2hos B   2 KRPRTAFSSEQLARLKREFNENRYLTERRRQQLSSELGLNEAQVKGWFKNMRAKIKKS  59
                                    11        21        31        41        51        

Chain C from PDB  Type:DNA  Length:21
                                                     
                 2hos C   1 TTTTGCCATGTAATCCCCGGA  21
                                    10        20 

Chain D from PDB  Type:DNA  Length:21
                                                     
                 2hos D  22 ATCCGGGGATTACATGGCAAA  42
                                    31        41 

   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (37, 37)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HMEN_DROME | P02836)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0000980    RNA polymerase II distal enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a RNA polymerase II (Pol II) distal enhancer. In mammalian cells, enhancers are distal sequences that increase the utilization of some promoters, and can function in either orientation and in any location (upstream or downstream) relative to the core promoter.
    GO:0001158    enhancer sequence-specific DNA binding    Interacting selectively and non-covalently with a specific sequence of DNA that is part of an enhancer, a transcription regulatory region that is somewhat distal from the core promoter and which enhances transcription from that promoter.
    GO:0001078    proximal promoter DNA-binding transcription repressor activity, RNA polymerase II-specific    A protein or a member of a complex that interacts selectively and non-covalently with a specific DNA sequence (sometimes referred to as a motif) within a proximal promoter regulatory region of a RNA polymerase II-transcribed gene to repress or decrease 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.
biological process
    GO:0007487    analia development    The process whose specific outcome is the progression of the analia over time, from its formation to the mature structure. The analia is the posterior-most vertral appendage that develops from the genital disc. An example of this process is analia development in Drosophila melanogaster.
    GO:0021960    anterior commissure morphogenesis    Generation of a long process of a CNS neuron, that carries efferent (outgoing) action potentials from the cell body in one half of the cerebral cortex towards target cells in the contralateral half. This axonal process is a member of those that make up the anterior commissure, a small midline fiber tract that lies at the anterior end of the corpus callosum.
    GO:0035288    anterior head segmentation    Partitioning the insect head anlage into procephalic (labral, (ocular), antennal and intercalary) segments. The procephalic segments lie anterior to the gnathal (posterior head) segments, and are pattered by different segmentation gene cascades to the abdominal, thoracic and posterior head (gnathal) segments.
    GO:0048099    anterior/posterior lineage restriction, imaginal disc    Formation and/or maintenance of a lineage boundary between anterior and posterior compartments that cells cannot cross, thus separating the populations of cells in each compartment.
    GO:0007448    anterior/posterior pattern specification, imaginal disc    The establishment, maintenance and elaboration of the anterior/posterior axis of the imaginal disc. Imaginal discs are epithelial infoldings in the larvae of holometabolous insects that rapidly develop into adult appendages during metamorphosis from larval to adult form.
    GO:0007411    axon guidance    The chemotaxis process that directs the migration of an axon growth cone to a specific target site in response to a combination of attractive and repulsive cues.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0007386    compartment pattern specification    The regionalization process in which embryonic segments are divided into compartments that will result in differences in cell differentiation.
    GO:0035224    genital disc anterior/posterior pattern formation    The establishment, maintenance and elaboration of the anterior/posterior axis of the genital disc. An anterior and posterior compartment form in each of the three genital disc primoridia (the female genital disc primordium, the male genital disc primordium and the anal primordium).
    GO:0035215    genital disc development    Progression of the genital imaginal disc over time, from its initial formation through to its metamorphosis to form the adult terminalia, comprising the entire set of internal and external genitalia and analia. Both sexes of Drosophila have a single genital disc formed from the female and male genital primordia, and the anal primordium. The anal primordium develops in both sexes, forming either male or female analia. However, only one of the genital primordia develops in each sex, forming either the male or the female genitalia.
    GO:0008406    gonad development    The process whose specific outcome is the progression of the gonad over time, from its formation to the mature structure. The gonad is an animal organ that produces gametes; in some species it also produces hormones.
    GO:0007447    imaginal disc pattern formation    The regionalization process that results in defined areas of the imaginal disc that will undergo specific cell differentaiton. Imaginal discs are epithelial infoldings in the larvae of holometabolous insects that develop into adult appendages (legs, antennae, wings, etc.) during metamorphosis from larval to adult form.
    GO:0007486    imaginal disc-derived female genitalia development    The process whose specific outcome is the progression of the female genitalia over time, from formation as part of the genital disc to the mature structure. An example of this is found in Drosophila melanogaster.
    GO:0007485    imaginal disc-derived male genitalia development    The process whose specific outcome is the progression of the male genitalia over time, from formation as part of the genital disc to the mature structure. An example of this is found in Drosophila melanogaster.
    GO:0007474    imaginal disc-derived wing vein specification    The regionalization process in which the area of a imaginal disc-derived wing that will form a wing vein is specified.
    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: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 by RNA polymerase II    Any process that stops, prevents, or reduces the frequency, rate or extent of transcription mediated by RNA polymerase II.
    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:0007400    neuroblast fate determination    The cell fate determination process in which a cell becomes capable of differentiating autonomously into a neuroblast cell regardless of its environment; upon determination, the cell fate cannot be reversed. An example of this process is found in Mus musculus.
    GO:0045944    positive regulation of transcription by RNA polymerase II    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0007388    posterior compartment specification    The process involved in the specification of cell identity in the posterior compartments of the segmented embryo.
    GO:0035289    posterior head segmentation    Partitioning the posterior region of the insect head anlage into gnathal (mandibular, maxillary and labial) segments. Unlike the anterior head (procephalic) segments, formation of the posterior head (gnathal) segments occurs by a similar mechanism to trunk segmentation, where a cascade of gap genes, pair-rule genes and segment-polarity genes subdivide the embryo into progressively smaller domains.
    GO:0010468    regulation of gene expression    Any process that modulates 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:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0007367    segment polarity determination    Division of the 14 parasegments of the embryo into anterior and posterior compartments; exemplified by the actions of the segment polarity gene products.
    GO:0035277    spiracle morphogenesis, open tracheal system    The process in which the anatomical structures of a spiracle are generated and organized. Spiracles are the openings in the insect open tracheal system; externally they connect to the epidermis and internally they connect to the tracheal trunk.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0035290    trunk segmentation    Partitioning of the blastoderm embryo into trunk segmental units. In Drosophila, the trunk segments include thoracic segments and abdominal segments A1 to A8.
    GO:0007418    ventral midline development    The process whose specific outcome is the progression of the ventral midline over time, from its formation to the mature structure. In protostomes (such as insects, snails and worms) as well as deuterostomes (vertebrates), the midline is an embryonic region that functions in patterning of the adjacent nervous tissue. The ventral midline in insects is a cell population extending along the ventral surface of the embryo and is the region from which cells detach to form the ventrally located nerve cords. In vertebrates, the midline is originally located dorsally. During development, it folds inwards and becomes the ventral part of the dorsally located neural tube and is then called the ventral midline, or floor plate.
    GO:0048100    wing disc anterior/posterior pattern formation    The establishment, maintenance and elaboration of the anterior/posterior axis of the wing disc, a precursor to the wing.
cellular component
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HMEN_DROME | P028361du0 1enh 1hdd 1p7i 1p7j 1ztr 2hdd 2hot 2jwt 2p81 3hdd

(-) Related Entries Specified in the PDB File

2hdd ENGRAILED HOMEODOMAIN Q50K MUTANT BOUND TO IDENTICAL DNA
2hot