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(-) Description

Title :  CRYSTAL STRUCTURE OF TRIM24 PHD-BROMODOMAIN COMPLEXED WITH 1-METHYL-5-(2-METHYL-1 3-THIAZOL-4-YL)-2 3-DIHYDRO-1H-INDOL-2-ONE (1)
 
Authors :  G. Poncet-Montange, W. Palmer, P. Jones
Date :  17 Feb 15  (Deposition) - 24 Jun 15  (Release) - 09 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
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: 562
    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  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
14CN2Ligand/Ion1-METHYL-5-(2-METHYL-1,3-THIAZOL-4-YL)-1,3-DIHYDRO-2H-INDOL-2-ONE
2SO42Ligand/IonSULFATE ION
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
14CN1Ligand/Ion1-METHYL-5-(2-METHYL-1,3-THIAZOL-4-YL)-1,3-DIHYDRO-2H-INDOL-2-ONE
2SO41Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
14CN1Ligand/Ion1-METHYL-5-(2-METHYL-1,3-THIAZOL-4-YL)-1,3-DIHYDRO-2H-INDOL-2-ONE
2SO41Ligand/IonSULFATE ION
3ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:829 , CYS A:832 , HIS A:849 , CYS A:852binding site for residue ZN A 1101
2AC2SOFTWARECYS A:841 , CYS A:844 , CYS A:867 , CYS A:870binding site for residue ZN A 1102
3AC3SOFTWAREALA A:923 , VAL A:928 , VAL A:932 , TYR A:935 , ASN A:980 , HOH A:1301binding site for residue 4CN A 1103
4AC4SOFTWARETRP A:828 , ASN A:834 , GLY A:835 , GLY B:835 , GLY B:836binding site for residue SO4 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
7AC7SOFTWAREALA B:923 , VAL B:928 , PRO B:929 , TYR B:935 , ASN B:980 , HOH B:1269binding site for residue 4CN B 1103
8AC8SOFTWARELYS B:950 , ARG B:951binding site for residue SO4 B 1104

(-) SS Bonds  (0, 0)

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

(-) 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 4YAB)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YAB)

(-) 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:178
                                                                                                                                                                                                                   
               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
                4yab A  823 SPNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   832       842       852       862       872       882 ||    898       908       918       928       938       948       958       968       978       988       998        
                                                                                       884|                                                                                                                   
                                                                                        891                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:174
                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...............ee......ee...........................................hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhh....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                4yab B  824 PNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   833       843       853       863       873       892       902       912       922       932       942       952       962       972       982       992      1002    
                                                                                   881|                                                                                                                   
                                                                                    891
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  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 4YAB)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 42)

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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 4yad 4yat 4yax 4ybm 4ybs 4ybt 4yc9 4zql 5h1t 5h1u 5h1v

(-) Related Entries Specified in the PDB File

4yad 4yat 4yax 4ybm 4ybs 4ybt 4yc9