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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN HDAC2 COMPLEXED WITH AN N-(2-AMINOPHENYL) BENZAMIDE
 
Authors :  R. J. Skene, A. J. Jennings
Date :  24 Mar 10  (Deposition) - 28 Apr 10  (Release) - 19 May 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.05
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Class 2, Hdac, Foot Pocket, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. C. Bressi, A. J. Jennings, R. Skene, Y. Wu, R. Melkus, R. De Jong, S. O'Connell, C. E. Grimshaw, M. Navre, A. R. Gangloff
Exploration Of The Hdac2 Foot Pocket: Synthesis And Sar Of Substituted N-(2-Aminophenyl)Benzamides.
Bioorg. Med. Chem. Lett. V. 20 3142 2010
PubMed-ID: 20392638  |  Reference-DOI: 10.1016/J.BMCL.2010.03.091

(-) Compounds

Molecule 1 - HISTONE DEACETYLASE 2
    ChainsA, B, C
    EC Number3.5.1.98
    EngineeredYES
    Expression SystemUNIDENTIFIED BACULOVIRUS
    Expression System StrainSF9
    Expression System Taxid10469
    Expression System Vector TypePSXB19
    GeneHDAC2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHD2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric Unit (5, 13)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2LLX3Ligand/IonN-(4-AMINOBIPHENYL-3-YL)BENZAMIDE
3NA3Ligand/IonSODIUM ION
4NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
5ZN3Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2LLX1Ligand/IonN-(4-AMINOBIPHENYL-3-YL)BENZAMIDE
3NA-1Ligand/IonSODIUM ION
4NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2LLX1Ligand/IonN-(4-AMINOBIPHENYL-3-YL)BENZAMIDE
3NA-1Ligand/IonSODIUM ION
4NHE-1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
5ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2LLX1Ligand/IonN-(4-AMINOBIPHENYL-3-YL)BENZAMIDE
3NA-1Ligand/IonSODIUM ION
4NHE-1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
5ZN-1Ligand/IonZINC ION

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:181 , HIS A:183 , ASP A:269 , LLX A:400BINDING SITE FOR RESIDUE ZN A 379
02AC2SOFTWAREASP A:179 , ASP A:181 , HIS A:183 , SER A:202 , PHE A:203BINDING SITE FOR RESIDUE CA A 380
03AC3SOFTWAREPHE A:192 , THR A:195 , VAL A:198 , TYR A:227 , HOH A:396 , HOH A:425BINDING SITE FOR RESIDUE NA A 381
04AC4SOFTWARETYR A:29 , MET A:35 , ARG A:39 , GLY A:143 , LEU A:144 , HIS A:145 , HIS A:146 , GLY A:154 , PHE A:155 , CYS A:156 , ASP A:181 , HIS A:183 , PHE A:210 , ASP A:269 , LEU A:276 , GLY A:305 , GLY A:306 , TYR A:308 , ZN A:379BINDING SITE FOR RESIDUE LLX A 400
05AC5SOFTWARETYR A:59 , LYS A:128 , HOH A:537 , HOH A:538 , HOH A:539 , ASP B:21 , GLY B:22 , ASP B:23 , ARG B:60 , GLU B:113 , LEU B:117BINDING SITE FOR RESIDUE NHE A 383
06AC6SOFTWAREASP B:181 , HIS B:183 , ASP B:269 , LLX B:400BINDING SITE FOR RESIDUE ZN B 379
07AC7SOFTWAREASP B:179 , ASP B:181 , HIS B:183 , SER B:202 , PHE B:203BINDING SITE FOR RESIDUE CA B 380
08AC8SOFTWAREPHE B:192 , THR B:195 , VAL B:198 , TYR B:227 , HOH B:385 , HOH B:441BINDING SITE FOR RESIDUE NA B 381
09AC9SOFTWARETYR B:29 , MET B:35 , ARG B:39 , GLY B:143 , LEU B:144 , HIS B:145 , HIS B:146 , GLY B:154 , PHE B:155 , CYS B:156 , ASP B:181 , HIS B:183 , PHE B:210 , ASP B:269 , GLY B:305 , GLY B:306 , TYR B:308 , ZN B:379BINDING SITE FOR RESIDUE LLX B 400
10BC1SOFTWAREASP C:181 , HIS C:183 , ASP C:269 , LLX C:400BINDING SITE FOR RESIDUE ZN C 379
11BC2SOFTWAREASP C:179 , ASP C:181 , HIS C:183 , SER C:202 , PHE C:203BINDING SITE FOR RESIDUE CA C 380
12BC3SOFTWAREPHE C:192 , THR C:195 , VAL C:198 , TYR C:227 , HOH C:389 , HOH C:464BINDING SITE FOR RESIDUE NA C 381
13BC4SOFTWARETYR C:29 , MET C:35 , ARG C:39 , GLY C:143 , LEU C:144 , HIS C:145 , HIS C:146 , GLY C:154 , PHE C:155 , CYS C:156 , ASP C:181 , HIS C:183 , PHE C:210 , ASP C:269 , LEU C:276 , GLY C:305 , GLY C:306 , TYR C:308 , ZN C:379BINDING SITE FOR RESIDUE LLX C 400

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3MAX)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:210 -Pro A:211
2Gly A:343 -Pro A:344
3Phe B:210 -Pro B:211
4Gly B:343 -Pro B:344
5Phe C:210 -Pro C:211
6Gly C:343 -Pro C:344

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 6)

Asymmetric Unit (2, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_025311R230CHDAC2_HUMANPolymorphism1042903A/B/CR234C
2UniProtVAR_025312Y315HHDAC2_HUMANPolymorphism17852888A/B/CY319H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_025311R230CHDAC2_HUMANPolymorphism1042903AR234C
2UniProtVAR_025312Y315HHDAC2_HUMANPolymorphism17852888AY319H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_025311R230CHDAC2_HUMANPolymorphism1042903BR234C
2UniProtVAR_025312Y315HHDAC2_HUMANPolymorphism17852888BY319H

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 3 (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_025311R230CHDAC2_HUMANPolymorphism1042903CR234C
2UniProtVAR_025312Y315HHDAC2_HUMANPolymorphism17852888CY319H

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3MAX)

(-) Exons   (0, 0)

(no "Exon" information available for 3MAX)

(-) 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:367
 aligned with HDAC2_HUMAN | Q92769 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:367
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       
          HDAC2_HUMAN     8 GKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRML 374
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.hhhhhhh.........hhhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee...............hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------H----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3max A  12 AKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRML 378
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       

Chain B from PDB  Type:PROTEIN  Length:364
 aligned with HDAC2_HUMAN | Q92769 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:364
                                    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       330       340       350       360       370    
          HDAC2_HUMAN    11 KVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRML 374
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee...hhhhh.........hhhhhhhhhhhhhhhhhhh.eee.....hhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhhh....eeeee.....hhhhhhhh.....eeeeeeee...............hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------H----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3max B  15 KVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRML 378
                                    24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374    

Chain C from PDB  Type:PROTEIN  Length:366
 aligned with HDAC2_HUMAN | Q92769 from UniProtKB/Swiss-Prot  Length:488

    Alignment length:366
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368      
          HDAC2_HUMAN     9 KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRML 374
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee...hhhhh.........hhhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee...............hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------C------------------------------------------------------------------------------------H----------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3max C  13 KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRML 378
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372      

   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 3MAX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MAX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3MAX)

(-) Gene Ontology  (78, 78)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C   (HDAC2_HUMAN | Q92769)
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: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: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:0031072    heat shock protein binding    Interacting selectively and non-covalently with a heat shock protein, any protein synthesized or activated in response to heat shock.
    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: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: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: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:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
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:0048149    behavioral response to ethanol    Any process that results in a change in the behavior of an organism as a result of an ethanol stimulus.
    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:0003300    cardiac muscle hypertrophy    The enlargement or overgrowth of all or part of the heart muscle due to an increase in size of cardiac muscle cells without cell division.
    GO:1903351    cellular response to dopamine    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a dopamine stimulus.
    GO:0034605    cellular response to heat    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a heat stimulus, a temperature stimulus above the optimal temperature for that organism.
    GO:0070301    cellular response to hydrogen peroxide    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hydrogen peroxide (H2O2) stimulus.
    GO:0071300    cellular response to retinoic acid    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a retinoic acid stimulus.
    GO:0071560    cellular response to transforming growth factor beta stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a transforming growth factor beta stimulus.
    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:0016358    dendrite development    The process whose specific outcome is the progression of the dendrite over time, from its formation to the mature structure. A dendrite is a freely branching protoplasmic process of a nerve cell.
    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:0006344    maintenance of chromatin silencing    The maintenance of chromatin in a transcriptionally silent state such as heterochromatin.
    GO:0043392    negative regulation of DNA binding    Any process that stops or reduces the frequency, rate or extent of DNA binding. DNA binding is any process in which a gene product interacts selectively with DNA (deoxyribonucleic acid).
    GO:0045347    negative regulation of MHC class II biosynthetic process    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of MHC class II.
    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:0061000    negative regulation of dendritic spine development    Any process that decreases the rate, frequency, or extent of dendritic spine development, the process whose specific outcome is the progression of the dendritic spine over time, from its formation to the mature structure.
    GO:0010977    negative regulation of neuron projection development    Any process that decreases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:2000757    negative regulation of peptidyl-lysine acetylation    Any process that stops, prevents or reduces the frequency, rate or extent of peptidyl-lysine acetylation.
    GO:0043433    negative regulation of sequence-specific DNA binding transcription factor activity    Any process that stops, prevents, or reduces the frequency, rate or extent of the activity of a transcription factor, any factor involved in the initiation or regulation of transcription.
    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:0032967    positive regulation of collagen biosynthetic process    Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of collagen, any of a group of fibrous proteins of very high tensile strength that form the main component of connective tissue in animals.
    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:0032732    positive regulation of interleukin-1 production    Any process that activates or increases the frequency, rate, or extent of interleukin-1 production.
    GO:0048714    positive regulation of oligodendrocyte differentiation    Any process that activates or increases the frequency, rate or extent of oligodendrocyte differentiation.
    GO:0045862    positive regulation of proteolysis    Any process that activates or increases the frequency, rate or extent of the hydrolysis of a peptide bond or bonds within a protein.
    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:0032760    positive regulation of tumor necrosis factor production    Any process that activates or increases the frequency, rate, or extent of tumor necrosis factor production.
    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:0001975    response to amphetamine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an amphetamine stimulus. Amphetamines consist of a group of compounds related to alpha-methylphenethylamine.
    GO:0031000    response to caffeine    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 caffeine stimulus. Caffeine is an alkaloid found in numerous plant species, where it acts as a natural pesticide that paralyzes and kills certain insects feeding upon them.
    GO:0042220    response to cocaine    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 cocaine stimulus. Cocaine is a crystalline alkaloid obtained from the leaves of the coca plant.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0055093    response to hyperoxia    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 stimulus indicating increased oxygen tension.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0035094    response to nicotine    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 nicotine stimulus.
    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.
cellular component
    GO:0035098    ESC/E(Z) complex    A multimeric protein complex that can methylate lysine-27 and lysine-9 residues of histone H3. In Drosophila the core subunits of the complex include ESC, E(Z), CAF1 (NURF-55) and SU(Z)12. In mammals the core subunits of the complex include EED, EZH2, SUZ12 and RBBP4.
    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: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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        HDAC2_HUMAN | Q927694lxz 4ly1 5iwg 5ix0

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