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(-) Description

Title :  COMPLEX STRUCTURE OF TRIM24 PHD-BROMODOMAIN AND INHIBITOR 1
 
Authors :  J. Liu
Date :  11 Oct 16  (Deposition) - 22 Feb 17  (Release) - 19 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (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, C, D
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 14)

Asymmetric Unit (3, 14)
No.NameCountTypeFull Name
17FF4Ligand/IonMETHYL 6-AZANYL-3,4-DIHYDRO-2H-QUINOLINE-1-CARBOXYLATE
2DMS2Ligand/IonDIMETHYL SULFOXIDE
3ZN8Ligand/IonZINC ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
17FF1Ligand/IonMETHYL 6-AZANYL-3,4-DIHYDRO-2H-QUINOLINE-1-CARBOXYLATE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
17FF1Ligand/IonMETHYL 6-AZANYL-3,4-DIHYDRO-2H-QUINOLINE-1-CARBOXYLATE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
17FF1Ligand/IonMETHYL 6-AZANYL-3,4-DIHYDRO-2H-QUINOLINE-1-CARBOXYLATE
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3ZN-1Ligand/IonZINC ION
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
17FF1Ligand/IonMETHYL 6-AZANYL-3,4-DIHYDRO-2H-QUINOLINE-1-CARBOXYLATE
2DMS-1Ligand/IonDIMETHYL SULFOXIDE
3ZN-1Ligand/IonZINC ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:829 , CYS A:832 , HIS A:849 , CYS A:852binding site for residue ZN A 1101
02AC2SOFTWARECYS A:841 , CYS A:844 , CYS A:867 , CYS A:870binding site for residue ZN A 1102
03AC3SOFTWAREALA A:923 , PHE A:924 , PRO A:929 , PHE A:979 , ASN A:980 , VAL A:986 , HOH A:1208binding site for residue 7FF A 1103
04AC4SOFTWARELYS A:846 , PHE A:914 , TYR A:956 , TYR A:996 , HOH A:1215binding site for residue DMS A 1104
05AC5SOFTWARECYS B:829 , CYS B:832 , HIS B:849 , CYS B:852binding site for residue ZN B 1101
06AC6SOFTWARECYS B:841 , CYS B:844 , CYS B:867 , CYS B:870binding site for residue ZN B 1102
07AC7SOFTWAREALA B:923 , PHE B:924 , ASN B:980 , HOH B:1203binding site for residue 7FF B 1103
08AC8SOFTWAREPRO B:902 , ARG B:906binding site for residue DMS B 1104
09AC9SOFTWARECYS C:841 , CYS C:844 , CYS C:867 , CYS C:870binding site for residue ZN C 1101
10AD1SOFTWARECYS C:829 , CYS C:832 , HIS C:849 , CYS C:852binding site for residue ZN C 1102
11AD2SOFTWAREALA C:923 , PHE C:924 , PRO C:929 , ASN C:980 , HOH C:1207binding site for residue 7FF C 1103
12AD3SOFTWARECYS D:829 , CYS D:832 , HIS D:849 , CYS D:852binding site for residue ZN D 1101
13AD4SOFTWARECYS D:841 , CYS D:844 , CYS D:867 , CYS D:870binding site for residue ZN D 1102
14AD5SOFTWAREALA D:923 , VAL D:928 , PRO D:929 , PHE D:979 , ASN D:980 , HOH D:1215binding site for residue 7FF D 1103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H1T)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Val A:854 -Pro A:855
2Val B:854 -Pro B:855
3Val C:854 -Pro C:855
4Val D:854 -Pro D:855

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H1T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H1T)

(-) Exons   (0, 0)

(no "Exon" information available for 5H1T)

(-) 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:172
                                                                                                                                                                                                             
               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
                5h1t A  825 NEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   834       844       854       864       874      |894       904       914       924       934       944       954       964       974       984       994      1004  
                                                                                  881|                                                                                                                  
                                                                                   892                                                                                                                  


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.............hhhhhhhhhhhhhhhhhh..hhhhhh.......hhhhhh....hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5h1t B  826 EDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAPSEKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   835       845       855       865       875       885||     898       908       918       928       938       948       958       968       978       988       998        
                                                                                      886|                                                                                                                    
                                                                                       890                                                                                                                    


Chain C 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
                5h1t C  824 PNEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDCDAPKKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   833       843       853       863       873       883 ||    898       908       918       928       938       948       958       968       978       988       998        
                                                                                       885|                                                                                                                   
                                                                                        891                                                                                                                   


Chain D from PDB  Type:PROTEIN  Length:172
                                                                                                                                                                                                             
               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
                5h1t D  825 NEDWCAVCQNGGELLCCEKCPKVFHLSCHVPTLTNFPSGEWICTFCRDLSKPEVEYDKKTEGLVKLTPIDKRKCERLLLFLYCHEMSLAFQDPVPLTVPDYYKIIKNPMDLSTIKKRLQEDYSMYSKPEDFVADFRLIFQNCAEFNEPDSEVANAGIKLENYFEELLKNLYP 1006
                                   834       844       854       864       874      |894       904       914       924       934       944       954       964       974       984       994      1004  
                                                                                  881|                                                                                                                  
                                                                                   892
   Legend:   → Mismatch (orange background)
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    → 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 5H1T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H1T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H1T)

(-) Gene Ontology  (42, 42)

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  5h1t
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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 5h1u 5h1v

(-) Related Entries Specified in the PDB File

5h1u 5h1v