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(-) Description

Title :  CRYSTAL STRUCTURE OF CHROMOBOX HOMOLOGY 7 (CBX7) WITH SETDB1-1170ME3 PEPTIDE
 
Authors :  C. Ren, A. N. Plotnikov, M. M. Zhou
Date :  01 Dec 14  (Deposition) - 04 Mar 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.60
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Cbx7, Chromodomain, Transcription (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Ren, K. Morohashi, A. N. Plotnikov, J. Jakoncic, S. G. Smith, J. Li, L. Zeng, Y. Rodriguez, V. Stojanoff, M. Walsh, M. M. Zhou
Small-Molecule Modulators Of Methyl-Lysine Binding For The Cbx7 Chromodomain.
Chem. Biol. V. 22 161 2015
PubMed-ID: 25660273  |  Reference-DOI: 10.1016/J.CHEMBIOL.2014.11.021

(-) Compounds

Molecule 1 - CHROMOBOX PROTEIN HOMOLOG 7
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 7-66
    GeneCBX7, D15ERTD417E
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
 
Molecule 2 - SETDB1-1170ME3 PEPTIDE
    ChainsC, D
    EngineeredYES
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A  D
Biological Unit 2 (1x) BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric Unit (3, 8)
No.NameCountTypeFull Name
1CIT4Ligand/IonCITRIC ACID
2FE2Ligand/IonFE (III) ION
3M3L2Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2FE-1Ligand/IonFE (III) ION
3M3L1Mod. Amino AcidN-TRIMETHYLLYSINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1CIT2Ligand/IonCITRIC ACID
2FE-1Ligand/IonFE (III) ION
3M3L1Mod. Amino AcidN-TRIMETHYLLYSINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECIT A:102 , CIT B:102binding site for residue FE A 101
2AC2SOFTWAREARG A:20 , ARG A:22 , TRP A:42 , FE A:101 , HOH A:217 , HOH A:273 , HOH A:275 , HOH A:291 , LYS B:23 , ARG B:52 , CIT B:102 , ARG C:1165binding site for residue CIT A 102
3AC3SOFTWAREVAL A:21 , ARG A:22 , LYS A:23 , GLY A:24 , LEU A:49 , ASP A:50 , HOH A:221 , HOH A:224 , ARG B:22 , FE B:101 , CIT B:103 , HOH B:228 , ARG D:1165 , GLY D:1166 , PHE D:1167binding site for residue CIT A 103
4AC4SOFTWARECIT A:103 , HOH A:224 , CIT B:103binding site for residue FE B 101
5AC5SOFTWAREARG A:22 , FE A:101 , CIT A:102 , VAL B:21 , ARG B:22 , LYS B:23 , GLY B:24 , LEU B:49 , ASP B:50 , HOH B:217 , ARG C:1165 , GLY C:1166 , PHE C:1167binding site for residue CIT B 102
6AC6SOFTWARELYS A:23 , ARG A:52 , CIT A:103 , ARG B:20 , ARG B:22 , TRP B:42 , FE B:101 , HOH B:211 , HOH B:220 , HOH B:229 , HOH B:261 , HOH B:268 , HOH B:281binding site for residue CIT B 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X3S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X3S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X3S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X3S)

(-) Exons   (0, 0)

(no "Exon" information available for 4X3S)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:61
                                                                                              
               SCOP domains ------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------- Transcript
                4x3s A    6 MGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEERDRA   66
                                    15        25        35        45        55        65 

Chain B from PDB  Type:PROTEIN  Length:60
                                                                                             
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeeeeeeeeeeee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                4x3s B    6 MGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEERDR   65
                                    15        25        35        45        55        65

Chain C from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..eeeeee. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                4x3s C 1165 RGFALkSTH 1173
                                 |   
                              1170-M3L

Chain D from PDB  Type:PROTEIN  Length:9
                                          
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ..eeeeee. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                4x3s D 1165 RGFALkSTH 1173
                                 |   
                              1170-M3L

   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 4X3S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X3S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X3S)

(-) Gene Ontology  (33, 38)

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 Related Entries

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

UniProtKB/Swiss-Prot
        CBX7_MOUSE | Q8VDS32kvm 4x3k 4x3t 4x3u 5ejw
        SETB1_HUMAN | Q150473dlm 5kch 5kco 5ke2 5ke3 5kh6

(-) Related Entries Specified in the PDB File

4x3t 4x3u