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(-) Description

Title :  CRYSTAL STRUCTURE OF THE BCL6 BTB DOMAIN IN COMPLEX WITH F1324
 
Authors :  S. Sogabe, K. Ida, W. Lane, G. Snell
Date :  18 Nov 16  (Deposition) - 07 Dec 16  (Release) - 18 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Transcription Repressor, Complex, Inhibitor, Transcription-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Sakamoto, S. Sogabe, Y. Kamada, N. Sakai, K. Asano, M. Yoshimatsu, K. Ida, Y. Imaeda, J. I. Sakamoto
Discovery Of High-Affinity Bcl6-Binding Peptide And Its Structure-Activity Relationship.
Biochem. Biophys. Res. V. 482 310 2017 Commun.
PubMed-ID: 27856253  |  Reference-DOI: 10.1016/J.BBRC.2016.11.060

(-) Compounds

Molecule 1 - B-CELL LYMPHOMA 6 PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    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
 
Molecule 2 - F1324 PEPTIDE
    Chains: C, D
    Engineered: YES
    Organism Scientific: ENTEROBACTERIA PHAGE T7
    Organism Taxid: 10760
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:24 , ARG A:28 , HOH A:1004 , ARG C:811 , ARG D:811binding site for residue SO4 A 901
2AC2SOFTWAREARG B:24 , ARG C:811 , HOH C:909binding site for residue SO4 B 901

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5H7G)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5H7G)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5H7G)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5H7G)

(-) Exons   (0, 0)

(no "Exon" information available for 5H7G)

(-) 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:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhh........eee.....hhhhhhhhhhhhhhhee.....hhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h7g A   7 SCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKAS 128
                                    16        26        36        46        56        66        76        86        96       106       116       126  


Chain B from PDB  Type:PROTEIN  Length:122
                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhhhhhhh.....eeeee..eeeeehhhhhhhhhhhhhhhhh........eee.....hhhhhhhhhhhhhhheee....hhhhhhhhhhhh.hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------- Transcript
                 5h7g B   7 SCIQFTRHASDVLLNLNRLRSRDILTDVVIVVSREQFRAHKTVLMACSGLFYSIFTDQLKCNLSVINLDPEINPEGFCILLDFMYTSRLNLREGNIMAVMATAMYLQMEHVVDTCRKFIKAS 128
                                    16        26        36        46        56        66        76        86        96       106       116       126  


Chain C from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .eee......... Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5h7g C 801 LWYTDIRMSWRVP 813
                                   810   


Chain D from PDB  Type:PROTEIN  Length:13
                                             
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .eee......... Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                 5h7g D 801 LWYTDIRMSWRVP 813
                                   810
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → 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 5H7G)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5H7G)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5H7G)

(-) Gene Ontology  (59, 59)

Asymmetric/Biological Unit(hide GO term definitions)

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  5h7g
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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 5h7h 5n1x 5n1z 5n20 5n21 5x4m 5x4n 5x4o 5x4p 5x4q

(-) Related Entries Specified in the PDB File

5h7h