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(-) Description

Title :  CRYSTAL STRUCTURE OF TRIM24 PHD-BROMODOMAIN COMPLEXED WITH N-[6-(4-METHOXYPHENOXY)-1,3-DIMETHYL-2-OXO-2,3-DIHYDRO-1H-1,3-BENZODIAZOL-5-YL]BENZENESULFONAMIDE (5G)
 
Authors :  G. Poncet-Montange, W. Palmer, P. Jones
Date :  18 Feb 15  (Deposition) - 24 Jun 15  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Center For Biomolecular Structure And Function, Bromodomain, Trim24, Inhibitor, Transcription-Transcription Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. S. Palmer, G. Poncet-Montange, G. Liu, A. Petrocchi, N. Reyna, G. Subramanian, J. Theroff, A. Yau, M. Kost-Alimova, J. P. Bardenhagen, E. Leo, H. E. Shepard, T. N. Tieu, X. Shi, Y. Zhan, S. Zhao, M. C. Barton, G. Draetta, C. Toniatti, P. Jones, M. Geck Do, J. N. Andersen
Structure-Guided Design Of Iacs-9571, A Selective High-Affinity Dual Trim24-Brpf1 Bromodomain Inhibitor.
J. Med. Chem. V. 59 1440 2016
PubMed-ID: 26061247  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B00405

(-) Compounds

Molecule 1 - TRANSCRIPTION INTERMEDIARY FACTOR 1-ALPHA
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSFDUET-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: BROMODOMAIN (UNP RESIDUES 824-1006)
    Gene: TRIM24, RNF82, TIF1, TIF1A
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: TIF1-ALPHA,E3 UBIQUITIN-PROTEIN LIGASE TRIM24,RING FINGER PROTEIN 82,TRIPARTITE MOTIF-CONTAINING PROTEIN 24

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
14AE2Ligand/IonN-[6-(4-METHOXYPHENOXY)-1,3-DIMETHYL-2-OXO-2,3-DIHYDRO-1H-BENZIMIDAZOL-5-YL]BENZENESULFONAMIDE
2GOL1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
4ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
14AE1Ligand/IonN-[6-(4-METHOXYPHENOXY)-1,3-DIMETHYL-2-OXO-2,3-DIHYDRO-1H-BENZIMIDAZOL-5-YL]BENZENESULFONAMIDE
2GOL1Ligand/IonGLYCEROL
3SO4-1Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
14AE1Ligand/IonN-[6-(4-METHOXYPHENOXY)-1,3-DIMETHYL-2-OXO-2,3-DIHYDRO-1H-BENZIMIDAZOL-5-YL]BENZENESULFONAMIDE
2GOL-1Ligand/IonGLYCEROL
3SO41Ligand/IonSULFATE ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:922 , ALA A:923 , VAL A:928 , PRO A:929 , VAL A:932 , PHE A:979 , ASN A:980 , VAL A:986 , HOH A:1304 , LEU B:930binding site for residue 4AE A 1101
2AC2SOFTWARECYS A:841 , CYS A:844 , CYS A:867 , CYS A:870binding site for residue ZN A 1102
3AC3SOFTWARECYS A:829 , CYS A:832 , HIS A:849 , CYS A:852binding site for residue ZN A 1103
4AC4SOFTWARETRP A:828 , ASN A:834 , GLY A:835 , ASP B:827 , GLY B:835 , GLY B:836binding site for residue GOL A 1104
5AC5SOFTWARECYS B:829 , CYS B:832 , HIS B:849 , CYS B:852binding site for residue ZN B 1101
6AC6SOFTWARECYS B:841 , CYS B:844 , CYS B:867 , CYS B:870binding site for residue ZN B 1102
7AC7SOFTWARELYS B:950 , ARG B:951binding site for residue SO4 B 1103
8AC8SOFTWARELEU A:930 , ALA B:923 , VAL B:928 , PRO B:929 , PHE B:979 , ASN B:980 , HOH B:1265binding site for residue 4AE B 1104

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YAX)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Val A:854 -Pro A:855
2Val B:854 -Pro B:855

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YAX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YAX)

(-) Exons   (0, 0)

(no "Exon" information available for 4YAX)

(-) 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:180
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................ee......ee...............................hhhhh............hhhhhhhhhhhhhhhhhh..hhhhhh.......hhhhhh....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4yax A  823 SPNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAPSKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   832       842       852       862       872       882   ||  896       906       916       926       936       946       956       966       976       986       996      1006
                                                                                         886|                                                                                                                   
                                                                                          891                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:178
                                                                                                                                                                                                                   
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee......ee...............................hhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4yax B  824 PNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAPKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   833       843       853       863       873       883 ||    898       908       918       928       938       948       958       968       978       988       998        
                                                                                       885|                                                                                                                   
                                                                                        891
   Legend:   → Mismatch (orange background)
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  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 4YAX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YAX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YAX)

(-) Gene Ontology  (42, 42)

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  6.3.2.-
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 Related Entries

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

UniProtKB/Swiss-Prot
        TIF1A_HUMAN | O15164: 2yyn 3o33 3o34 3o35 3o36 3o37 4yab 4yad 4yat 4ybm 4ybs 4ybt 4yc9 4zql 5h1t 5h1u 5h1v

(-) Related Entries Specified in the PDB File

4yab 4yad 4yat 4ybm 4ybs 4ybt