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Title :  STRUCTURE OF HISTONE DEACETYLASE 1
 
Authors :  S. C. Mallena, H. Sindhu, B. Gayatri, P. R. Praveen
Date :  08 Jul 04  (Deposition) - 27 Jul 04  (Release) - 27 Jul 04  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Hydrolase, Nuclear Protein, Chromatin Regulator, Transcription Regulation, Repressor, Ubl Conjugation (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. C. Mallena, H. Sindhu, B. Gayatri, P. R. Praveen
Structure Of Histone Deacetylase 1
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISTONE DEACETYLASE 1
    ChainsA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    SynonymHD1

 Structural Features

(-) Chains, Units

  
Theoretical Model 

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 1TYI)

(-) Sites  (0, 0)

(no "Site" information available for 1TYI)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1TYI)

(-) Exons   (10, 10)

Theoretical Model (10, 10)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003735481aENSE00001850850chr1:32757687-32757819133HDAC1_HUMAN1-17171A:1-88
1.2ENST000003735482ENSE00001759703chr1:32768222-32768334113HDAC1_HUMAN17-54381A:8-4538
1.3ENST000003735483ENSE00000916604chr1:32782266-32782383118HDAC1_HUMAN55-94401A:46-8540
1.4ENST000003735484ENSE00001049603chr1:32790080-3279015475HDAC1_HUMAN94-119261A:85-11026
1.5aENST000003735485aENSE00001049601chr1:32792540-32792678139HDAC1_HUMAN119-165471A:110-15647
1.5gENST000003735485gENSE00001049604chr1:32793137-32793278142HDAC1_HUMAN165-212481A:156-20348
1.6bENST000003735486bENSE00002156228chr1:32794669-3279476193HDAC1_HUMAN213-243311A:204-23431
1.7cENST000003735487cENSE00001692609chr1:32796179-32796287109HDAC1_HUMAN244-280371A:235-27137
1.8bENST000003735488bENSE00001770293chr1:32796369-32796509141HDAC1_HUMAN280-327481A:271-31848
1.9aENST000003735489aENSE00001758736chr1:32797075-32797183109HDAC1_HUMAN327-363371A:318-32710
1.10bENST0000037354810bENSE00001756323chr1:32797277-32797407131HDAC1_HUMAN363-407450--
1.10dENST0000037354810dENSE00001682220chr1:32797691-32797843153HDAC1_HUMAN407-458520--
1.11ENST0000037354811ENSE00001802592chr1:32798302-3279835049HDAC1_HUMAN458-474170--
1.12cENST0000037354812cENSE00001905176chr1:32798618-32799236619HDAC1_HUMAN474-48290--

(-) Sequences/Alignments

Theoretical Model
   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:327
 aligned with HDAC1_HUMAN | Q13547 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:327
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       
          HDAC1_HUMAN    10 KVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEY 336
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhh...........hhhhhhhhhhhhh..hhh.ee.....hhhhhhh..hhhhhhhhhhhhhhh....hhhhhhh............hhhhhhhhhhhhhhhhhhhhh...eeee...................hhhhhhhhhhhh....eeeee.....hhhhhhhhh....eeeeeeee...............hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhh...eeeee.hhhhh..........hhhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) 1.1a    -------------------------------------Exon 1.3  PDB: A:46-85 UniProt: 55-94   ------------------------Exon 1.5a  PDB: A:110-156 UniProt: 119-165     -----------------------------------------------Exon 1.6b  PDB: A:204-234      Exon 1.7c  PDB: A:235-271            ----------------------------------------------Exon 1.9a  Transcript 1 (1)
           Transcript 1 (2) -------Exon 1.2  PDB: A:8-45 UniProt: 17-54  ---------------------------------------Exon 1.4  PDB: A:85-110   ---------------------------------------------Exon 1.5g  PDB: A:156-203 UniProt: 165-212      -------------------------------------------------------------------Exon 1.8b  PDB: A:271-318 UniProt: 280-327      --------- Transcript 1 (2)
                 1tyi A   1 KVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEY 327
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       

   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  (0, 0)

(no "SCOP Domain" information available for 1TYI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1TYI)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (65, 65)

Theoretical Model(hide GO term definitions)
Chain A   (HDAC1_HUMAN | Q13547)
molecular function
    GO:0032041    NAD-dependent histone deacetylase activity (H3-K14 specific)    Catalysis of the reaction: histone H3 N6-acetyl-L-lysine (position 14) + H2O = histone H3 L-lysine (position 14) + acetate. This reaction requires the presence of NAD, and represents the removal of an acetyl group from lysine at position 14 of the histone H3 protein.
    GO:0051059    NF-kappaB binding    Interacting selectively and non-covalently with NF-kappaB, a transcription factor for eukaryotic RNA polymerase II promoters.
    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: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:0001103    RNA polymerase II repressing transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription repressing factor, a protein involved in negative regulation of transcription.
    GO:0001106    RNA polymerase II transcription corepressor activity    Interacting selectively and non-covalently with an RNA polymerase II repressing transcription factor and also with the RNA polymerase II basal transcription machinery in order to stop, prevent, or reduce the frequency, rate or extent of transcription. Cofactors generally do not bind DNA, but rather mediate protein-protein interactions between repressive transcription factors and the basal transcription machinery.
    GO:0001085    RNA polymerase II transcription factor binding    Interacting selectively and non-covalently with an RNA polymerase II transcription factor, any protein required to initiate or regulate transcription by RNA polymerase II.
    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:0001047    core promoter binding    Interacting selectively and non-covalently with the regulatory region composed of the transcription start site and binding sites for the basal transcription machinery. 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:0019213    deacetylase activity    Catalysis of the hydrolysis of an acetyl group or groups from a substrate molecule.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0004407    histone deacetylase activity    Catalysis of the reaction: histone N6-acetyl-L-lysine + H2O = histone L-lysine + acetate. This reaction represents the removal of an acetyl group from a histone, a class of proteins complexed to DNA in chromatin and chromosomes.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0031492    nucleosomal DNA binding    Interacting selectively and non-covalently with the DNA portion of a nucleosome.
    GO:0047485    protein N-terminus binding    Interacting selectively and non-covalently with a protein N-terminus, the end of any peptide chain at which the 2-amino (or 2-imino) function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    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:0033558    protein deacetylase activity    Catalysis of the hydrolysis of an acetyl group or groups from a protein substrate.
    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: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:0000976    transcription 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 transcription of that section of the DNA. The transcribed region might be described as a gene, cistron, or operon.
biological process
    GO:0043044    ATP-dependent chromatin remodeling    Dynamic structural changes to eukaryotic chromatin that require energy from the hydrolysis of ATP, ranging from local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation, mediated by ATP-dependent chromatin-remodelling factors.
    GO:1904837    beta-catenin-TCF complex assembly    The aggregation, arrangement and bonding together of a set of components to form a beta-catenin-TCF complex.
    GO:0007596    blood coagulation    The sequential process in which the multiple coagulation factors of the blood interact, ultimately resulting in the formation of an insoluble fibrin clot; it may be divided into three stages: stage 1, the formation of intrinsic and extrinsic prothrombin converting principle; stage 2, the formation of thrombin; stage 3, the formation of stable fibrin polymers.
    GO:0006338    chromatin remodeling    Dynamic structural changes to eukaryotic chromatin occurring throughout the cell division cycle. These changes range from the local changes necessary for transcriptional regulation to global changes necessary for chromosome segregation.
    GO:0032922    circadian regulation of gene expression    Any process that modulates the frequency, rate or extent of gene expression such that an expression pattern recurs with a regularity of approximately 24 hours.
    GO:0042733    embryonic digit morphogenesis    The process, occurring in the embryo, by which the anatomical structures of the digit are generated and organized. A digit is one of the terminal divisions of an appendage, such as a finger or toe.
    GO:0009913    epidermal cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epidermal cell, any of the cells making up the epidermis.
    GO:0061029    eyelid development in camera-type eye    The progression of the eyelid in a camera-type eye from its formation to the mature state. The eyelid is a membranous cover that helps protect and lubricate the eye.
    GO:0061198    fungiform papilla formation    The developmental process pertaining to the initial formation of a spongiform papilla from unspecified parts. The fungiform papilla is a mushroom-shaped papilla of the tongue.
    GO:0060789    hair follicle placode formation    The developmental process in which a hair placode forms. An hair follicle placode is a thickening of the ectoderm that will give rise to the hair follicle bud.
    GO:0070932    histone H3 deacetylation    The modification of histone H3 by the removal of one or more acetyl groups.
    GO:0070933    histone H4 deacetylation    The modification of histone H4 by the removal of one or more acetyl groups.
    GO:0016575    histone deacetylation    The modification of histones by removal of acetyl groups.
    GO:0043922    negative regulation by host of viral transcription    Any process in which a host organism stops, prevents, or reduces the frequency, rate or extent of viral transcription.
    GO:0060766    negative regulation of androgen receptor signaling pathway    Any process that decreases the rate, frequency, or extent of the androgen receptor signaling pathway.
    GO:0043066    negative regulation of apoptotic process    Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
    GO:0090090    negative regulation of canonical Wnt signaling pathway    Any process that decreases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    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:0010832    negative regulation of myotube differentiation    Any process that decreases the frequency, rate or extent of myotube differentiation. Myotube differentiation is the process in which a relatively unspecialized cell acquires specialized features of a myotube cell. Myotubes are multinucleated cells that are formed when proliferating myoblasts exit the cell cycle, differentiate and fuse.
    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:0042475    odontogenesis of dentin-containing tooth    The process whose specific outcome is the progression of a dentin-containing tooth over time, from its formation to the mature structure. A dentin-containing tooth is a hard, bony organ borne on the jaw or other bone of a vertebrate, and is composed mainly of dentin, a dense calcified substance, covered by a layer of enamel.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0010870    positive regulation of receptor biosynthetic process    Any process that increases the frequency or rate of receptor biosynthesis. Receptor biosynthesis is the collection of chemical reactions and pathways resulting in the formation of a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    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:0006476    protein deacetylation    The removal of an acetyl group from a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
    GO:1901796    regulation of signal transduction by p53 class mediator    Any process that modulates the frequency, rate or extent of signal transduction by p53 class mediator.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0048511    rhythmic process    Any process pertinent to the generation and maintenance of rhythms in the physiology of an organism.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
    GO:0016581    NuRD complex    An approximately 2 MDa multi-subunit complex that exhibits ATP-dependent chromatin remodeling activity in addition to histone deacetylase (HDAC) activity, and has been shown to establish transcriptional repression of a number of target genes in vertebrates, invertebrates and fungi. Amongst its subunits, the NuRD complex contains histone deacetylases, histone binding proteins and Mi-2-like proteins.
    GO:0016580    Sin3 complex    A multiprotein complex that functions broadly in eukaryotic organisms as a transcriptional repressor of protein-coding genes, through the gene-specific deacetylation of histones. Amongst its subunits, the Sin3 complex contains Sin3-like proteins, and a number of core proteins that are shared with the NuRD complex (including histone deacetylases and histone binding proteins). The Sin3 complex does not directly bind DNA itself, but is targeted to specific genes through protein-protein interactions with DNA-binding proteins.
    GO:0000785    chromatin    The ordered and organized complex of DNA, protein, and sometimes RNA, that forms the chromosome.
    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:0000118    histone deacetylase complex    A protein complex that possesses histone deacetylase activity.
    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.

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        HDAC1_HUMAN | Q135474bkx 5icn

(-) Related Entries Specified in the PDB File

1c3p