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(-) Description

Title :  CRYSTAL STRUCTURE OF TRIM24 WITH 3,4-DIMETHOXY-N-(6-(4-METHOXYPHENOXY)-1,3-DIMETHYL-2-OXO-2,3-DIHYDRO-1H-BENZO[D]IMIDAZOL-5-YL)BENZENESULFONAMIDE INHIBITOR
 
Authors :  C. Tallant, Structural Genomics Consortium (Sgc), P. G. K. Clark, L. C. C. Vieira, T. Krojer, G. Nunez-Alonso, S. Picaud, O. Fedorov, D. J F. Von Delft, C. H. Arrowsmith, A. M. Edwards, C. Bountra, P. E. Brenna
Date :  10 May 15  (Deposition) - 17 Jun 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.79
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transcriptional Coactivator, Histone H3 Modifications, E3 Protein- Ubiquitin Ligase Activity, Structural Genomics, Structural Genomics Consortium, Sgc, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. G. Clark, L. C. Vieira, C. Tallant, O. Fedorov, D. C. Singleton, C. M. Rogers, O. P. Monteiro, J. M. Bennett, R. Baronio, S. Muller, D. L. Daniels, J. Mendez, S. Knapp, P. E. Brennan, D. J. Dixon
Crystal Structure Of Trim24 With 3, 4-Dimethoxy-N-(6-(4-Methoxyphenoxy)-1, 3-Dimethyl-2-Oxo-2, 3-Dihydro-1H-Benzo[D]Imidazol-5-Yl)Benzenesulfonamide Inhibitor
To Be Published
PubMed: search

(-) 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: PET15
    Expression System Taxid: 562
    Fragment: RESIDUES 791-972
    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  (5, 9)

Asymmetric Unit (5, 9)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
24QH1Ligand/Ion3,4-DIMETHOXY-N-[6-(4-METHOXYPHENOXY)-1,3-DIMETHYL-2-OXO-2,3-DIHYDRO-1H-BENZIMIDAZOL-5-YL]BENZENESULFONAMIDE
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4SO42Ligand/IonSULFATE ION
5ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
11PE-1Ligand/IonPENTAETHYLENE GLYCOL
24QH-1Ligand/Ion3,4-DIMETHOXY-N-[6-(4-METHOXYPHENOXY)-1,3-DIMETHYL-2-OXO-2,3-DIHYDRO-1H-BENZIMIDAZOL-5-YL]BENZENESULFONAMIDE
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4SO41Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
11PE1Ligand/IonPENTAETHYLENE GLYCOL
24QH1Ligand/Ion3,4-DIMETHOXY-N-[6-(4-METHOXYPHENOXY)-1,3-DIMETHYL-2-OXO-2,3-DIHYDRO-1H-BENZIMIDAZOL-5-YL]BENZENESULFONAMIDE
3DMS-1Ligand/IonDIMETHYL SULFOXIDE
4SO41Ligand/IonSULFATE ION
5ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
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
3AC3SOFTWAREPRO A:902 , ARG A:906 , HOH A:1242binding site for residue SO4 A 1103
4AC4SOFTWAREALA A:923 , ASN A:980 , HOH A:1217binding site for residue DMS 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
7AC7SOFTWARELEU A:930 , TYR A:936 , LEU B:922 , ALA B:923 , PHE B:924 , VAL B:928 , VAL B:932 , PHE B:979 , ASN B:980 , HOH B:1212 , HOH B:1268binding site for residue 4QH B 1103
8AC8SOFTWAREPRO B:902 , ARG B:906binding site for residue SO4 B 1104
9AC9SOFTWARELYS B:846 , GLU B:895 , GLY B:896 , PHE B:914 , TYR B:956 , HOH B:1238binding site for residue 1PE B 1105

(-) SS Bonds  (0, 0)

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

(-) 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 4ZQL)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZQL)

(-) 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:177
                                                                                                                                                                                                                  
               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
                4zql A  824 MNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   833       843       853       863       873       883||     899       909       919       929       939       949       959       969       979       989       999       
                                                                                      884|                                                                                                                   
                                                                                       891                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:176
                                                                                                                                                                                                                 
               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
                4zql B  824 MNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   833       843       853       863       873       883||     900       910       920       930       940       950       960       970       980       990      1000      
                                                                                      884|                                                                                                                  
                                                                                       892
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4ZQL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (42, 42)

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

(-) Related Entries Specified in the PDB File

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