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(-) Description

Title :  CRYSTAL STRUCTURE OF CHROMOBOX HOMOLOG 7 (CBX7) CHROMODOMAIN WITH MS37452
 
Authors :  C. Ren, J. Jakoncic, M. M. Zhou
Date :  01 Dec 14  (Deposition) - 04 Mar 15  (Release) - 04 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.14
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,F  (1x)
Biol. Unit 3:  D,E  (1x)
Keywords :  Cbx7, Chromodomain, Ms37452, Inhibitor, 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
    Chains: A, B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 7-66
    Gene: CBX7, D15ERTD417E
    Organism Common: MOUSE
    Organism Scientific: MUS MUSCULUS
    Organism Taxid: 10090

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABCDEF
Biological Unit 1 (1x): AB    
Biological Unit 2 (1x):   C  F
Biological Unit 3 (1x):    DE 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 16)

Asymmetric Unit (3, 16)
No.NameCountTypeFull Name
145E6Ligand/Ion1-[4-(2,3-DIMETHOXYBENZOYL)PIPERAZIN-1-YL]-2-(3-METHYLPHENOXY)ETHANONE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3ZN9Ligand/IonZINC ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
145E2Ligand/Ion1-[4-(2,3-DIMETHOXYBENZOYL)PIPERAZIN-1-YL]-2-(3-METHYLPHENOXY)ETHANONE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
145E2Ligand/Ion1-[4-(2,3-DIMETHOXYBENZOYL)PIPERAZIN-1-YL]-2-(3-METHYLPHENOXY)ETHANONE
2EDO1Ligand/Ion1,2-ETHANEDIOL
3ZN-1Ligand/IonZINC ION
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
145E2Ligand/Ion1-[4-(2,3-DIMETHOXYBENZOYL)PIPERAZIN-1-YL]-2-(3-METHYLPHENOXY)ETHANONE
2EDO-1Ligand/Ion1,2-ETHANEDIOL
3ZN-1Ligand/IonZINC ION

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:6 , VAL A:13 , TRP A:32 , TRP A:35 , TYR A:39 , THR A:41 , GLU A:43 , HIS A:47 , HOH A:224 , HOH A:226 , GLU B:46 , LEU B:49 , 45E C:101binding site for residue 45E A 101
02AC2SOFTWAREHIS A:47 , HIS B:47 , HOH B:249binding site for residue ZN A 102
03AC3SOFTWAREHIS A:5 , MET A:6binding site for residue ZN A 103
04AC4SOFTWAREGLU A:46 , LEU A:49 , PHE B:11 , TRP B:32 , TYR B:39 , THR B:41 , GLU B:43 , HIS B:47 , HOH B:213 , HOH B:246binding site for residue 45E B 101
05AC5SOFTWAREHOH A:252 , HIS B:5 , HOH B:247binding site for residue ZN B 102
06AC6SOFTWARETYR A:39 , 45E A:101 , MET C:6 , PHE C:11 , VAL C:13 , TRP C:32 , TRP C:35 , TYR C:39 , THR C:41 , GLU C:43 , HIS C:47 , HOH C:218 , GLU F:46 , LEU F:49binding site for residue 45E C 101
07AC7SOFTWAREHIS C:47 , HOH C:219 , HOH C:224 , HIS F:47 , HOH F:213 , HOH F:215binding site for residue ZN C 102
08AC8SOFTWAREHIS C:5 , HOH C:225 , HOH F:212binding site for residue ZN C 103
09AC9SOFTWAREVAL D:10 , PHE D:11 , TRP D:32 , TRP D:35 , TYR D:39 , GLU D:43 , ZN D:102 , HOH D:221 , HOH D:232 , TRP E:32 , GLU E:46 , HIS E:47 , ILE E:48 , 45E E:101binding site for residue 45E D 101
10AD1SOFTWAREHIS D:47 , 45E D:101 , HOH D:221 , HIS E:47 , 45E E:101 , HOH E:227binding site for residue ZN D 102
11AD2SOFTWAREHIS D:5 , HOH D:229 , HOH D:243binding site for residue ZN D 103
12AD3SOFTWAREVAL A:21 , VAL D:13 , GLU D:46 , HIS D:47 , PRO D:51 , 45E D:101 , ZN D:102 , PHE E:11 , TRP E:32 , TRP E:35 , TYR E:39 , GLU E:43 , HOH E:206 , HOH E:210 , HOH E:217 , HOH E:227binding site for residue 45E E 101
13AD4SOFTWAREHIS E:5 , MET E:6binding site for residue ZN E 102
14AD5SOFTWAREGLU C:46 , LEU C:49 , HOH C:220 , MET F:6 , PHE F:11 , VAL F:13 , TRP F:32 , TRP F:35 , THR F:41 , GLU F:43 , HIS F:47 , HOH F:221binding site for residue 45E F 101
15AD6SOFTWAREHOH C:223 , HIS F:5 , HOH F:201 , HOH F:204 , HOH F:218binding site for residue ZN F 102
16AD7SOFTWARELEU C:49 , VAL F:13 , HIS F:47 , ILE F:48 , LEU F:49 , ASP F:50 , HOH F:214 , HOH F:223binding site for residue EDO F 103

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4X3T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4X3T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4X3T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4X3T)

(-) Exons   (0, 0)

(no "Exon" information available for 4X3T)

(-) 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:62
                                                                                             
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  4x3t A  5 HMGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEERDRA 66
                                    14        24        34        44        54        64  


Chain B from PDB  Type:PROTEIN  Length:60
                                                                                           
               SCOP domains ------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------ Pfam domains
         Sec.struct. author ........eeeeeeeeee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------ Transcript
                  4x3t B  5 HMGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEERD 64
                                    14        24        34        44        54        64


Chain C from PDB  Type:PROTEIN  Length:62
                                                                                             
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee..eeeeeeee...hhhhheeee.hhh.hhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  4x3t C  5 HMGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEERDRA 66
                                    14        24        34        44        54        64  


Chain D from PDB  Type:PROTEIN  Length:62
                                                                                             
               SCOP domains -------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhh...eeeeeeeeee..eeeeeeee...hhhhheeeehhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------- Transcript
                  4x3t D  5 HMGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEKEERDRA 66
                                    14        24        34        44        54        64  


Chain E from PDB  Type:PROTEIN  Length:51
                                                                                  
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..eeeeeeeeee..eeeeeeee...hhhhheeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                  4x3t E  5 HMGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVM 55
                                    14        24        34        44        54 


Chain F from PDB  Type:PROTEIN  Length:56
                                                                                       
               SCOP domains -------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeeeeeeeee..eeeeeeee...hhhhheeee.hhh..hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------- Transcript
                  4x3t F  5 HMGEQVFAVESIRKKRVRKGKVEYLVKWKGWPPKYSTWEPEEHILDPRLVMAYEEK 60
                                    14        24        34        44        54
   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 4X3T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4X3T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4X3T)

(-) Gene Ontology  (16, 16)

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        CBX7_MOUSE | Q8VDS3: 2kvm 4x3k 4x3s 4x3u 5ejw

(-) Related Entries Specified in the PDB File

4x3s 4x3u