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(-) Description

Title :  COMPLEX STRUCTURE OF TRIM24 PHD-BROMODOMAIN AND INHIBITOR 6
 
Authors :  J. Liu
Date :  11 Oct 16  (Deposition) - 22 Feb 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Transcription Transcription Inhibitor, Transcription-Transcription Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Liu, F. Li, H. Bao, Y. Jiang, S. Zhang, R. Ma, J. Gao, J. Wu, K. Ruan
The Polar Warhead Of A Trim24 Bromodomain Inhibitor Rearranges A Water-Mediated Interaction Network
Febs J. V. 284 1082 2017
PubMed-ID: 28207202  |  Reference-DOI: 10.1111/FEBS.14041

(-) Compounds

Molecule 1 - TRANSCRIPTION INTERMEDIARY FACTOR 1-ALPHA
    Chains: A, B
    EC Number: 6.3.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Strain: 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Taxid: 866768
    Fragment: 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, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
17FU2Ligand/Ion2-HYDRAZINO-1,3-BENZOTHIAZOLE-6-CARBOHYDRAZIDE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3ZN4Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
17FU1Ligand/Ion2-HYDRAZINO-1,3-BENZOTHIAZOLE-6-CARBOHYDRAZIDE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
17FU1Ligand/Ion2-HYDRAZINO-1,3-BENZOTHIAZOLE-6-CARBOHYDRAZIDE
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3ZN-1Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
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 , PHE A:924 , VAL A:928 , VAL A:932 , TYR A:935 , ILE A:972 , ASN A:975 , CYS A:976 , ASN A:980 , HOH A:1219 , HOH A:1249binding site for residue 7FU A 1103
4AC4SOFTWAREPRO A:861 , SER A:862 , GLY A:863 , GLU A:981binding 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
7AC7SOFTWAREALA B:923 , PHE B:924 , VAL B:928 , VAL B:932 , TYR B:935 , ILE B:972 , ASN B:975 , CYS B:976 , ASN B:980 , HOH B:1213 , HOH B:1230 , HOH B:1234 , HOH B:1237binding site for residue 7FU B 1103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H1V)

(-) 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 5H1V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H1V)

(-) Exons   (0, 0)

(no "Exon" information available for 5H1V)

(-) 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:169
                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee......ee.........................................hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5h1v A  825 NEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQESMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   834       844       854       864       874     ||895       905       915       925       935       945       957       967       977       987       997         
                                                                                 880|                                                           954|                                                 
                                                                                  892                                                            957                                                 


Chain B from PDB  Type:PROTEIN  Length:170
                                                                                                                                                                                                           
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............ee......ee..........................................hhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5h1v B  825 NEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQESMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   834       844       854       864       874      |894       904       914       924       934       944       954|      966       976       986       996      1006
                                                                                  881|                                                           954|                                                 
                                                                                   892                                                            957
   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 5H1V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H1V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H1V)

(-) Gene Ontology  (42, 42)

Asymmetric Unit(hide GO term definitions)

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

(-) Related Entries Specified in the PDB File

5h1t 5h1u