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(-) Description

Title :  COMPLEX STRUCTURE OF PCAF BROMODOMAIN WITH SMALL CHEMICAL LIGAND NP1
 
Authors :  L. Zeng, J. Li, M. Muller, S. Yan, S. Mujtaba, C. Pan, Z. Wang, M. M. Zhou
Date :  07 Dec 04  (Deposition) - 16 Aug 05  (Release) - 24 Feb 09  (Revision)
Method :  SOLUTION NMR
Resolution :  NOT APPLICABLE
Chains :  NMR Structure  :  A
Keywords :  Bromodomain, Histone-Acetyltransferase, Nmr-Structure, Chemical Ligand (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Zeng, J. Li, M. Muller, S. Yan, S. Mujtaba, C. Pan, Z. Wang, M. M. Zhou
Selective Small Molecules Blocking Hiv-1 Tat And Coactivator Pcaf Association
J. Am. Chem. Soc. V. 127 2376 2005
PubMed-ID: 15724976  |  Reference-DOI: 10.1021/JA044885G
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HISTONE ACETYLATRANSFERASE PCAF
    ChainsA
    EC Number2.3.1.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET14B
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentBROMODOMAIN
    GenePCAF
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymP300/CBP-ASSOCIATED FACTOR, P/CAF, HISTONE ACETYLASE PCAF

 Structural Features

(-) Chains, Units

  
NMR Structure 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

NMR Structure (1, 1)
No.NameCountTypeFull Name
1NP11Ligand/IonN-(3-AMINOPROPYL)-4-METHYL-2-NITROBENZENAMINE

(-) Sites  (1, 1)

NMR Structure (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:750 , VAL A:752 , GLU A:756 , ALA A:757 , PRO A:758 , TYR A:802 , TYR A:809BINDING SITE FOR RESIDUE NP1 A 201

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

NMR Structure (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1BROMODOMAIN_2PS50014 Bromodomain profile.KAT2B_HUMAN740-810  1A:740-810
2BROMODOMAIN_1PS00633 Bromodomain signature.KAT2B_HUMAN745-802  1A:745-802

(-) Exons   (4, 4)

NMR Structure (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002637541aENSE00001189392chr3:20081515-20082272758KAT2B_HUMAN1-1011010--
1.2ENST000002637542ENSE00001076225chr3:20113825-20113951127KAT2B_HUMAN102-144430--
1.3ENST000002637543ENSE00001695585chr3:20136755-20136900146KAT2B_HUMAN144-192490--
1.4ENST000002637544ENSE00001076230chr3:20141354-2014144693KAT2B_HUMAN193-223310--
1.6ENST000002637546ENSE00001076222chr3:20142779-20142960182KAT2B_HUMAN224-284610--
1.7bENST000002637547bENSE00000755284chr3:20153088-20153279192KAT2B_HUMAN284-348650--
1.8aENST000002637548aENSE00000755443chr3:20156374-20156480107KAT2B_HUMAN348-384370--
1.9ENST000002637549ENSE00000755498chr3:20161090-20161215126KAT2B_HUMAN384-426430--
1.10bENST0000026375410bENSE00000755616chr3:20164160-20164296137KAT2B_HUMAN426-471460--
1.11ENST0000026375411ENSE00000755725chr3:20167397-20167605209KAT2B_HUMAN472-541700--
1.12aENST0000026375412aENSE00001800162chr3:20168915-20169041127KAT2B_HUMAN541-583430--
1.13ENST0000026375413ENSE00001076216chr3:20178434-20178544111KAT2B_HUMAN584-620370--
1.14ENST0000026375414ENSE00001076226chr3:20181713-20181856144KAT2B_HUMAN621-668480--
1.15aENST0000026375415aENSE00001076221chr3:20187808-20187922115KAT2B_HUMAN669-707390--
1.16ENST0000026375416ENSE00001076235chr3:20189455-2018949137KAT2B_HUMAN707-719131A:715-7195
1.17bENST0000026375417bENSE00001076223chr3:20189735-2018979864KAT2B_HUMAN719-740221A:719-74022
1.18aENST0000026375418aENSE00001076233chr3:20189895-2018997985KAT2B_HUMAN741-769291A:741-76929
1.19ENST0000026375419ENSE00001272618chr3:20193824-201958962073KAT2B_HUMAN769-832641A:769-83264

(-) 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:118
 aligned with KAT2B_HUMAN | Q92831 from UniProtKB/Swiss-Prot  Length:832

    Alignment length:118
                                   724       734       744       754       764       774       784       794       804       814       824        
          KAT2B_HUMAN   715 GKEKSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLIDK 832
               SCOP domains d1wuga_ A: P300/CAF histone acetyltransferase bromodomain                                                              SCOP domains
               CATH domains 1wugA00 A:715-832 Histone Acetyltransferase; Chain A                                                                   CATH domains
               Pfam domains -----------------Bromodomain-1wugA01 A:732-815                                                       ----------------- Pfam domains
         Sec.struct. author .........hhhhhhhhhhhhhhhhhhh..hhhhhh..................hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------BROMODOMAIN_2  PDB: A:740-810 UniProt: 740-810                         ---------------------- PROSITE (1)
                PROSITE (2) ------------------------------BROMODOMAIN_1  PDB: A:745-802 UniProt: 745-802            ------------------------------ PROSITE (2)
           Transcript 1 (1) 1.16 ---------------------Exon 1.18a  PDB: A:741-769   --------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----Exon 1.17b            ----------------------------Exon 1.19  PDB: A:769-832 UniProt: 769-832                       Transcript 1 (2)
                 1wug A 715 GSHMSKEPRDPDQLYSTLKSILQQVKSHQSAWPFMEPVKRTEAPGYYEVIRFPMDLKTMSERLKNRYYVSKKLFMADLQRVFTNCKEYNPPESEYYKCANILEKFFFSKIKEAGLIDK 832
                                   724       734       744       754       764       774       784       794       804       814       824        

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (1, 1)

NMR Structure

(-) CATH Domains  (1, 1)

NMR Structure

(-) Pfam Domains  (1, 1)

NMR Structure

(-) Gene Ontology  (59, 59)

NMR Structure(hide GO term definitions)
Chain A   (KAT2B_HUMAN | Q92831)
molecular function
    GO:0008080    N-acetyltransferase activity    Catalysis of the transfer of an acetyl group to a nitrogen atom on the acceptor molecule.
    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:0016407    acetyltransferase activity    Catalysis of the transfer of an acetyl group to an acceptor molecule.
    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:0004861    cyclin-dependent protein serine/threonine kinase inhibitor activity    Stops, prevents or reduces the activity of a cyclin-dependent protein serine/threonine kinase.
    GO:0004402    histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
    GO:0035035    histone acetyltransferase binding    Interacting selectively and non-covalently with the enzyme histone acetyltransferase.
    GO:0042826    histone deacetylase binding    Interacting selectively and non-covalently with the enzyme histone deacetylase.
    GO:0004468    lysine N-acetyltransferase activity, acting on acetyl phosphate as donor    Catalysis of the reaction: acetyl phosphate + L-lysine = phosphate + N6-acetyl-L-lysine.
    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:0032403    protein complex binding    Interacting selectively and non-covalently with any protein complex (a complex of two or more proteins that may include other nonprotein molecules).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0003713    transcription coactivator activity    Interacting selectively and non-covalently with a activating transcription factor and also with the basal transcription machinery in order to increase the frequency, rate or extent of transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between activating transcription factors and the basal transcription machinery.
    GO:0003712    transcription cofactor activity    Interacting selectively and non-covalently with a regulatory transcription factor and also with the basal transcription machinery in order to modulate transcription. Cofactors generally do not bind the template nucleic acid, but rather mediate protein-protein interactions between regulatory transcription factors and the basal transcription machinery.
    GO:0008134    transcription factor binding    Interacting selectively and non-covalently with a transcription factor, any protein required to initiate or regulate transcription.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016746    transferase activity, transferring acyl groups    Catalysis of the transfer of an acyl group from one compound (donor) to another (acceptor).
biological process
    GO:0018076    N-terminal peptidyl-lysine acetylation    The acetylation of the N-terminal lysine of proteins.
    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:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0007050    cell cycle arrest    A regulatory process that halts progression through the cell cycle during one of the normal phases (G1, S, G2, M).
    GO:0032869    cellular response to insulin 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 an insulin stimulus. Insulin is a polypeptide hormone produced by the islets of Langerhans of the pancreas in mammals, and by the homologous organs of other organisms.
    GO:0034599    cellular response to oxidative stress    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 oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
    GO:0071374    cellular response to parathyroid hormone 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 parathyroid hormone 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:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    GO:0043970    histone H3-K9 acetylation    The modification of histone H3 by the addition of an acetyl group to a lysine residue at position 9 of the histone.
    GO:0016573    histone acetylation    The modification of a histone by the addition of an acetyl group.
    GO:0018393    internal peptidyl-lysine acetylation    The addition of an acetyl group to a non-terminal lysine residue in a protein.
    GO:0007613    memory    The activities involved in the mental information processing system that receives (registers), modifies, stores, and retrieves informational stimuli. The main stages involved in the formation and retrieval of memory are encoding (processing of received information by acquisition), storage (building a permanent record of received information as a result of consolidation) and retrieval (calling back the stored information and use it in a suitable way to execute a given task).
    GO:0008285    negative regulation of cell proliferation    Any process that stops, prevents or reduces the rate or extent of cell proliferation.
    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:0018394    peptidyl-lysine acetylation    The acetylation of peptidyl-lysine.
    GO:0035563    positive regulation of chromatin binding    Any process that increases the frequency, rate or extent of chromatin binding. Chromatin binding is the selective interaction with chromatin, the network of fibers of DNA, protein, and sometimes RNA, that make up the chromosomes of the eukaryotic nucleus during interphase.
    GO:0045815    positive regulation of gene expression, epigenetic    Any epigenetic process that activates or increases the rate of gene expression.
    GO:0035948    positive regulation of gluconeogenesis by positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of gluconeogenesis by activating or increasing the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0071442    positive regulation of histone H3-K14 acetylation    Any process that activates or increases the frequency, rate or extent of the addition of an acetyl group to histone H3 at position 14 of the histone.
    GO:2000617    positive regulation of histone H3-K9 acetylation    Any process that activates or increases the frequency, rate or extent of histone H3-K9 acetylation.
    GO:0010976    positive regulation of neuron projection development    Any process that increases 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: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:0006473    protein acetylation    The addition of an acetyl group to a protein amino acid. An acetyl group is CH3CO-, derived from acetic [ethanoic] acid.
    GO:0010835    regulation of protein ADP-ribosylation    Any process that modulates the frequency, rate or extent of protein ADP-ribosylation. Protein ADP-ribosylation is the transfer, from NAD, of ADP-ribose to protein amino acids.
    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:0006367    transcription initiation from RNA polymerase II promoter    Any process involved in the assembly of the RNA polymerase II preinitiation complex (PIC) at an RNA polymerase II promoter region of a DNA template, resulting in the subsequent synthesis of RNA from that promoter. The initiation phase includes PIC assembly and the formation of the first few bonds in the RNA chain, including abortive initiation, which occurs when the first few nucleotides are repeatedly synthesized and then released. Promoter clearance, or release, is the transition between the initiation and elongation phases of transcription.
    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:0031672    A band    The dark-staining region of a sarcomere, in which myosin thick filaments are present; the center is traversed by the paler H zone, which in turn contains the M line.
    GO:0005671    Ada2/Gcn5/Ada3 transcription activator complex    A multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. Contains either GCN5 or PCAF in a mutually exclusive manner. The budding yeast complex includes Gcn5p, two proteins of the Ada family, and two TBP-associate proteins (TAFs); analogous complexes in other species have analogous compositions, and usually contain homologs of the yeast proteins. Both ATAC- or SAGA (see GO:0000124, SAGA complex) are involved in the acetylation of histone H3K9 and K14 residues.
    GO:0031674    I band    A region of a sarcomere that appears as a light band on each side of the Z disc, comprising a region of the sarcomere where thin (actin) filaments are not overlapped by thick (myosin) filaments; contains actin, troponin, and tropomyosin; each sarcomere includes half of an I band at each end.
    GO:0000125    PCAF complex    A large multiprotein complex that possesses histone acetyltransferase activity and is involved in regulation of transcription. The composition is similar to that of the SAGA complex, but includes fewer Spt and Ada proteins, and more TAFs.
    GO:0042641    actomyosin    Any complex of actin, myosin, and accessory proteins.
    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:0000123    histone acetyltransferase complex    A protein complex that possesses histone acetyltransferase activity.
    GO:0000776    kinetochore    A multisubunit complex that is located at the centromeric region of DNA and provides an attachment point for the spindle microtubules.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        KAT2B_HUMAN | Q928311cm0 1jm4 1n72 1wum 1zs5 2rnw 2rnx 3gg3 4nsq 5fdz 5fe0 5fe1 5fe2 5fe3 5fe4 5fe5 5fe6 5fe7 5fe8 5fe9 5lvq 5lvr

(-) Related Entries Specified in the PDB File

1b91 STRUCTURE AND LIGAND OF A HISTONE ACETYLTRANSFERASE BROMODOMAIN
1jm4 RECOGNITION OF HIV-1 TAT BY PCAF BROMODOMAIN
1wum THE SAME PROTEIN WITH SMALL CHEMICAL LIGAND NP2