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(-) Description

Title :  SET7/9 Y305F IN COMPLEX WITH TAF10 PEPTIDE AND ADOHCY
 
Authors :  P. A. Del Rizzo, J. -F. Couture, M. S. Roiko, B. S. Strunk, J. S. Brunzell L. M. Dirk, R. L. Houtz, R. C. Trievel
Date :  12 Mar 10  (Deposition) - 28 Jul 10  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ternary Complex, Set Domain, Methyltransferase, S-Adenosyl-L- Homocysteine, Taf10 Peptide, Chromatin Regulator, Chromosomal Protein, Nucleus, S-Adenosyl-L-Methionine, Transcription, Transcription Regulation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. A. Del Rizzo, J. F. Couture, L. M. Dirk, B. S. Strunk, M. S. Roiko, J. S. Brunzelle, R. L. Houtz, R. C. Trievel
Set7/9 Catalytic Mutants Reveal The Role Of Active Site Water Molecules In Lysine Multiple Methylation.
J. Biol. Chem. V. 285 31849 2010
PubMed-ID: 20675860  |  Reference-DOI: 10.1074/JBC.M110.114587

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SETD7
    ChainsA
    EC Number2.1.1.43
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHIS2
    Expression System StrainBL21(DE3)ROSETTA2
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 110-366
    GeneKIAA1717, KMT7, SET7, SET9, SETD7
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Strain9606
    SynonymHISTONE H3-K4 METHYLTRANSFERASE SETD7, H3-K4-HMTASE SETD7, SET DOMAIN-CONTAINING PROTEIN 7, SET7/9, LYSINE N-METHYLTRANSFERASE 7
 
Molecule 2 - TAF10 PEPTIDE
    ChainsB
    EngineeredYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:44 , HOH A:66 , HOH A:90 , ALA A:226 , GLU A:228 , GLY A:264 , ASN A:265 , HIS A:293 , LYS A:294 , ASN A:296 , HIS A:297 , TYR A:335 , TRP A:352 , GLU A:356 , HOH A:379 , HOH A:463 , HOH A:475 , HOH A:480BINDING SITE FOR RESIDUE SAH A 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3M54)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:279 -Pro A:280

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3M54)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SETPS50280 SET domain profile.SETD7_HUMAN214-336  1A:214-336

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002740311aENSE00001831410chr4:140477928-140477252677SETD7_HUMAN1-14140--
1.3ENST000002740313ENSE00001613109chr4:140468203-140468074130SETD7_HUMAN14-57440--
1.4aENST000002740314aENSE00001643989chr4:140454520-140454319202SETD7_HUMAN57-124681A:116-1249
1.5ENST000002740315ENSE00001671090chr4:140450374-140450185190SETD7_HUMAN125-188641A:125-18864
1.6ENST000002740316ENSE00001802218chr4:140444589-14044450882SETD7_HUMAN188-215281A:188-21528
1.7bENST000002740317bENSE00001663487chr4:140441548-140441431118SETD7_HUMAN215-254401A:215-25440
1.8ENST000002740318ENSE00001734092chr4:140439196-140439039158SETD7_HUMAN255-307531A:255-30753
1.9ENST000002740319ENSE00001192306chr4:140432997-1404271905808SETD7_HUMAN307-366601A:307-365 (gaps)59

(-) 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:245
 aligned with SETD7_HUMAN | Q8WTS6 from UniProtKB/Swiss-Prot  Length:366

    Alignment length:250
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365
          SETD7_HUMAN   116 HGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIYDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSPPGKSGPEAPEWYQVELKAFQATQQ 365
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains MORN-3m54A01 --------------------------------------------------------------------------------------------------SET-3m54A02 A:227-336                                                                                         ----------------------------- Pfam domains
         Sec.struct. author ...eeee.....eeee.........eeeeeee.....eeeeeeee..eeeeeeeeeeeeee..eeeeee.....ee.................hhhhhhheeeee.......eeeee........eeeee..eeehhhhhhh.hhhhh...ee.....eee..............hhhhhee.....eeeeeeee...eeeeeeee........eeee........-----...hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------SET  PDB: A:214-336 UniProt: 214-336                                                                                       ----------------------------- PROSITE
           Transcript 1 (1) Exon 1.4aExon 1.5  PDB: A:125-188 UniProt: 125-188                       --------------------------Exon 1.7b  PDB: A:215-254               Exon 1.8  PDB: A:255-307 UniProt: 255-307            ---------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------------------------------------Exon 1.6  PDB: A:188-215    -------------------------------------------------------------------------------------------Exon 1.9  PDB: A:307-365 (gaps) UniProt: 307-366            Transcript 1 (2)
                 3m54 A 116 HGVCWIYYPDGGSLVGEVNEDGEMTGEKIAYVYPDERTALYGKFIDGEMIEGKLATLMSTEEGRPHFELMPGNSVYHFDKSTSSCISTNALLPDPYESERVYVAESLISSAGEGLFSKVAVGPNTVMSFYNGVRITHQEVDSRDWALNGNTLSLDEETVIDVPEPYNHVSKYCASLGHKANHSFTPNCIFDMFVHPRFGPIKCIRTLRAVEADEELTVAYGYDHSP-----PEAPEWYQVELKAFQATQQ 365
                                   125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335     |   - |     355       365
                                                                                                                                                                                                                                                           341   347                  

Chain B from PDB  Type:PROTEIN  Length:9
 aligned with TAF10_HUMAN | Q12962 from UniProtKB/Swiss-Prot  Length:218

    Alignment length:9
          TAF10_HUMAN   185 RSKSKDRKY 193
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 3m54 B 185 xSKSKDRKY 193
                            |        
                          185-ACE    

   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 3M54)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3M54)

(-) Pfam Domains  (2, 2)

Asymmetric/Biological Unit
(-)
Clan: MORN (14)
(-)
Family: SET (46)

(-) Gene Ontology  (43, 48)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (SETD7_HUMAN | Q8WTS6)
molecular function
    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:0018024    histone-lysine N-methyltransferase activity    Catalysis of the reaction: S-adenosyl-L-methionine + histone L-lysine = S-adenosyl-L-homocysteine + histone N6-methyl-L-lysine. The methylation of peptidyl-lysine in histones forms N6-methyl-L-lysine, N6,N6-dimethyl-L-lysine and N6,N6,N6-trimethyl-L-lysine derivatives.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0002039    p53 binding    Interacting selectively and non-covalently with one of the p53 family of proteins.
    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:0016279    protein-lysine N-methyltransferase activity    Catalysis of the transfer of a methyl group from S-adenosyl-L-methionine to the epsilon-amino group of a lysine residue in a protein substrate.
    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.
biological process
    GO:0006974    cellular response to DNA damage 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 stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0070828    heterochromatin organization    Any process that results in the specification, formation or maintenance of the physical structure of eukaryotic heterochromatin, a compact and highly condensed form of chromatin.
    GO:0034968    histone lysine methylation    The modification of a histone by addition of one or more methyl groups to a lysine residue.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0018027    peptidyl-lysine dimethylation    The methylation of peptidyl-lysine to form peptidyl-N6,N6-dimethyl-L-lysine.
    GO:0018022    peptidyl-lysine methylation    The methylation of peptidyl-lysine to form either the mono-, di- or trimethylated derivative.
    GO:0018026    peptidyl-lysine monomethylation    The methylation of peptidyl-lysine to form peptidyl-N6-methyl-L-lysine.
    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:0051570    regulation of histone H3-K9 methylation    Any process that modulates the frequency, rate or extent of the covalent addition of a methyl group to the lysine at position 9 of histone H3.
    GO:0006355    regulation of transcription, DNA-templated    Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
    GO:0045471    response to ethanol    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 ethanol stimulus.
    GO:0006351    transcription, DNA-templated    The cellular synthesis of RNA on a template of DNA.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.

Chain B   (TAF10_HUMAN | Q12962)
molecular function
    GO:0070063    RNA polymerase binding    Interacting selectively and non-covalently with an RNA polymerase molecule or complex.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0030331    estrogen receptor binding    Interacting selectively and non-covalently with an estrogen receptor.
    GO:0004402    histone acetyltransferase activity    Catalysis of the reaction: acetyl-CoA + histone = CoA + acetyl-histone.
    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: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: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.
biological process
    GO:0006352    DNA-templated transcription, initiation    Any process involved in the assembly of the RNA polymerase preinitiation complex (PIC) at the core 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. The initiation phase ends just before and does not include promoter clearance, or release, which is the transition between the initiation and elongation phases of transcription.
    GO:0043966    histone H3 acetylation    The modification of histone H3 by the addition of an acetyl group.
    GO:0016578    histone deubiquitination    The modification of histones by removal of ubiquitin groups.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    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:0006368    transcription elongation from RNA polymerase II promoter    The extension of an RNA molecule after transcription initiation and promoter clearance at an RNA polymerase II promoter by the addition of ribonucleotides catalyzed by RNA polymerase II.
    GO:0006366    transcription from RNA polymerase II promoter    The synthesis of RNA from a DNA template by RNA polymerase II, originating at an RNA polymerase II promoter. Includes transcription of messenger RNA (mRNA) and certain small nuclear RNAs (snRNAs).
    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.
cellular component
    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:0030914    STAGA complex    A large multiprotein complex that possesses histone acetyltransferase and is involved in regulation of transcription. The composition is similar to that of the SAGA complex; for example, the human complex contains the transcription-transformation cofactor TRRAP, hGCN5L acetylase, novel human ADA-like and SPT-like cofactors, and a subset of TAFs.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    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:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.
    GO:0005669    transcription factor TFIID complex    A complex composed of TATA binding protein (TBP) and TBP associated factors (TAFs); the total mass is typically about 800 kDa. Most of the TAFs are conserved across species. In TATA-containing promoters for RNA polymerase II (Pol II), TFIID is believed to recognize at least two distinct elements, the TATA element and a downstream promoter element. TFIID is also involved in recognition of TATA-less Pol II promoters. Binding of TFIID to DNA is necessary but not sufficient for transcription initiation from most RNA polymerase II promoters.
    GO:0033276    transcription factor TFTC complex    A protein complex that does not contain either a TATA-binding protein (TBP) or a TBP-like factor, but is composed of several TAFIIs and other proteins, including a histone acetyltransferase. This complex is able to nucleate transcription initiation by RNA polymerase II, can mediate transcriptional activation, and has histone acetyltransferase activity.

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 Related Entries

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

UniProtKB/Swiss-Prot
        SETD7_HUMAN | Q8WTS61h3i 1mt6 1muf 1n6a 1n6c 1o9s 1xqh 2f69 3cbm 3cbo 3cbp 3m53 3m55 3m56 3m57 3m58 3m59 3m5a 3os5 3vuz 3vv0 4e47 4j7f 4j7i 4j83 4j8o 4jds 4jlg 5ayf 5eg2
        TAF10_HUMAN | Q129622f69 3m53 3m55 3m56 3m57 3m58 3m59 3m5a 4j7f 4j7i 4j83 4j8o 4wv4 5eg2

(-) Related Entries Specified in the PDB File

2f69 TERNARY COMPLEX OF SET7/9 BOUND TO ADOHCY AND A TAF10 PEPTIDE
3m53
3m55
3m56
3m57
3m58
3m59
3m5a