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(-) Description

Title :  CHROMODOMAIN ANTAGONISTS THAT TARGET THE POLYCOMB-GROUP METHYLLYSINE READER PROTEIN CHROMOBOX HOMOLOG 7 (CBX7)
 
Authors :  S. Chakravarthi, K. Daze, S. Douglas, T. Quon, A. Dev, F. Peng, M. Heller M. J. Boulanger, J. Wulff, F. Hof
Date :  09 Sep 13  (Deposition) - 02 Apr 14  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.54
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Chromobox Domain 7, Transcription Regulator (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Simhadri, K. D. Daze, S. F. Douglas, T. T. Quon, A. Dev, M. C. Gignac, F. Peng, M. Heller, M. J. Boulanger, J. E. Wulff, F. Hof
Chromodomain Antagonists That Target The Polycomb-Group Methyllysine Reader Protein Chromobox Homolog 7 (Cbx7).
J. Med. Chem. V. 57 2874 2014
PubMed-ID: 24625057  |  Reference-DOI: 10.1021/JM401487X

(-) Compounds

Molecule 1 - CHROMOBOX PROTEIN HOMOLOG 7
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: PROTEIN
    Gene: CBX7
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - PEPTIDE
    Chains: B
    Engineered: YES
    Fragment: PEPTIDE
    Organism Scientific: SYNTHETIC PEPTIDE
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 8)

Asymmetric/Biological Unit (6, 8)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2EDO3Ligand/Ion1,2-ETHANEDIOL
3M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
4MG1Ligand/IonMAGNESIUM ION
5NH21Mod. Amino AcidAMINO GROUP
6P331Ligand/Ion3,6,9,12,15,18-HEXAOXAICOSANE-1,20-DIOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:25 , TRP A:29 , PRO A:30BINDING SITE FOR RESIDUE EDO A 101
2AC2SOFTWARELYS A:32 , MET A:49 , GLU A:52 , HOH A:203 , HOH A:232BINDING SITE FOR RESIDUE EDO A 102
3AC3SOFTWARELYS A:27 , TRP A:29 , PRO A:45 , HOH B:103BINDING SITE FOR RESIDUE EDO A 103
4AC4SOFTWAREGLU A:2 , HIS A:41BINDING SITE FOR RESIDUE MG A 104
5AC5SOFTWARELYS A:12 , LYS A:13 , VAL A:15 , LEU A:23 , PRO A:31 , SER A:34 , GLU A:55 , HOH A:222BINDING SITE FOR RESIDUE P33 A 105

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4MN3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4MN3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4MN3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4MN3)

(-) Exons   (0, 0)

(no "Exon" information available for 4MN3)

(-) 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:56
                                                                                       
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee.eeeeeeeeee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  4mn3 A  1 GEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEE 56
                                    10        20        30        40        50      


Chain B from PDB  Type:PROTEIN  Length:7
                                      
               SCOP domains ------- SCOP domains
               CATH domains ------- CATH domains
               Pfam domains ------- Pfam domains
         Sec.struct. author ..ee... Sec.struct. author
                 SAPs(SNPs) ------- SAPs(SNPs)
                    PROSITE ------- PROSITE
                 Transcript ------- Transcript
                  4mn3 B  1 xFAYkSx  7
                            |   | |
                            1-ACE |
                                5-M3L
                                  7-NH2
   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 4MN3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4MN3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4MN3)

(-) Gene Ontology  (16, 16)

Asymmetric/Biological Unit(hide GO term definitions)

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  4mn3
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 Related Entries

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

UniProtKB/Swiss-Prot
        CBX7_HUMAN | O95931: 2k1b 2l12 2l1b 3gs2 5epj

(-) Related Entries Specified in the PDB File

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