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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BCL6 BTB DOMAIN IN COMPLEX WITH COMPOUND 7
 
Authors :  S. Sogabe, K. Ida, W. Lane, G. Snell
Date :  13 Feb 17  (Deposition) - 24 May 17  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Transcription Repressor, Transcription-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Kamada, N. Sakai, S. Sogabe, K. Ida, H. Oki, K. Sakamoto, W. Lane, G. Snell, M. Iida, Y. Imaeda, J. Sakamoto, J. Matsui
Discovery Of A B-Cell Lymphoma 6 Protein-Protein Interactio Inhibitor By A Biophysics-Driven Fragment-Based Approach
J. Med. Chem. V. 60 4358 2017
PubMed-ID: 28471657  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.7B00313

(-) Compounds

Molecule 1 - B-CELL LYMPHOMA 6 PROTEIN
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 5-129
    Gene: BCL6, BCL5, LAZ3, ZBTB27, ZNF51
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: BCL-6,B-CELL LYMPHOMA 5 PROTEIN,BCL-5,PROTEIN LAZ-3,ZINC FINGER AND BTB DOMAIN-CONTAINING PROTEIN 27,ZINC FINGER PROTEIN 51

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
17Z61Ligand/Ion5-[[5-CHLORANYL-2-(PYRIDIN-3-YLMETHYLAMINO)PYRIMIDIN-4-YL]AMINO]-1,3-DIHYDROINDOL-2-ONE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3K1Ligand/IonPOTASSIUM ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:21 , ARG A:24 , LEU A:25 , ARG A:28 , MET A:51 , ALA A:52 , CYS A:53 , GLY A:55 , TYR A:58 , GLN A:113 , GLU A:115 , EDO A:802binding site for residue 7Z6 A 801
2AC2SOFTWAREHIS A:14 , ASP A:17 , ALA A:52 , 7Z6 A:801 , HOH A:916binding site for residue EDO A 802
3AC3SOFTWARESER A:39 , PRO A:76 , GLU A:77 , ILE A:78binding site for residue K A 803

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5X4Q)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5X4Q)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X4Q)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X4Q)

(-) Exons   (0, 0)

(no "Exon" information available for 5X4Q)

(-) Sequences/Alignments

Asymmetric/Biological 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:130
                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.....eee.hhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhhh.hhhhh.eee.....hhhhhhhhhhhhhhh.......hhhhhhhhhhhh.hhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5x4q A   0 LYFQGADSCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKASE 129
                                     9        19        29        39        49        59        69        79        89        99       109       119       129
   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 5X4Q)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X4Q)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X4Q)

(-) Gene Ontology  (59, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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  5x4q
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  BCL6_HUMAN | P41182
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 Related Entries

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

UniProtKB/Swiss-Prot
        BCL6_HUMAN | P41182: 1r28 1r29 1r2b 2en2 2eos 2lce 2yrm 3bim 3e4u 3lbz 4cp3 4u2m 5h7g 5h7h 5n1x 5n1z 5n20 5n21 5x4m 5x4n 5x4o 5x4p

(-) Related Entries Specified in the PDB File

5x4m 5x4n 5x4o 5x4p