Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  STRUCTURE OF HUMAN G9A SET-DOMAIN (EHMT2) IN COMPLEX WITH INHIBITOR 13
 
Authors :  N. Babault, Y. Xiong, J. Liu, J. Jin
Date :  11 May 17  (Deposition) - 12 Jul 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein-Small Molecule Inhibitor Complex, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Xiong, F. Li, N. Babault, H. Wu, A. Dong, H. Zeng, X. Chen, C. H. Arrowsmith, P. J. Brown, J. Liu, M. Vedadi, J. Jin
Structure-Activity Relationship Studies Of G9A-Like Protein (Glp) Inhibitors.
Bioorg. Med. Chem. 2017
PubMed-ID: 28662962  |  Reference-DOI: 10.1016/J.BMC.2017.06.021

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE EHMT2
    Chains: A, B
    EC Number: 2.1.1.-, 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-LIC
    Expression System Strain: BL21 (DE3) CODON PLUS RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: G9A CATALYTIC SET-DOMAIN RESIDUES 916-1190
    Gene: EHMT2, BAT8, C6ORF30, G9A, KMT1C, NG36
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EUCHROMATIC HISTONE-LYSINE N-METHYLTRANSFERASE 2,HLA-B- ASSOCIATED TRANSCRIPT 8,HISTONE H3-K9 METHYLTRANSFERASE 3,H3-K9- HMTASE 3,LYSINE N-METHYLTRANSFERASE 1C,PROTEIN G9A

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
19HJ2Ligand/Ion6,7-DIMETHOXY-N~2~-METHYL-N~4~-(1-METHYLPIPERIDIN-4-YL)-N~2~-PROPYLQUINAZOLINE-2,4-DIAMINE
2SAM2Ligand/IonS-ADENOSYLMETHIONINE
3ZN8Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:980 , CYS A:1017 , CYS A:1023 , CYS A:1027binding site for residue ZN A 1501
02AC2SOFTWARECYS A:974 , CYS A:987 , CYS A:1017 , CYS A:1021binding site for residue ZN A 1502
03AC3SOFTWARECYS A:974 , CYS A:976 , CYS A:980 , CYS A:985binding site for residue ZN A 1503
04AC4SOFTWARECYS A:1115 , CYS A:1168 , CYS A:1170 , CYS A:1175binding site for residue ZN A 1504
05AC5SOFTWAREMET A:1048 , TRP A:1050 , SER A:1084 , TYR A:1085 , ARG A:1109 , PHE A:1110 , ASN A:1112 , HIS A:1113 , TYR A:1154 , PHE A:1166 , THR A:1167 , CYS A:1168 , GLN A:1169 , HOH A:1627 , HOH A:1634 , HOH A:1696 , HOH A:1723 , HOH A:1731binding site for residue SAM A 1505
06AC6SOFTWAREALA A:1077 , ASP A:1078 , ARG A:1080 , ASP A:1083 , LEU A:1086 , ASP A:1088 , CYS A:1098 , ARG A:1157 , PHE A:1158 , ILE A:1161binding site for residue 9HJ A 1506
07AC7SOFTWARECYS B:980 , CYS B:1017 , CYS B:1023 , CYS B:1027binding site for residue ZN B 1501
08AC8SOFTWARECYS B:974 , CYS B:987 , CYS B:1017 , CYS B:1021binding site for residue ZN B 1502
09AC9SOFTWARECYS B:974 , CYS B:976 , CYS B:980 , CYS B:985binding site for residue ZN B 1503
10AD1SOFTWARECYS B:1115 , CYS B:1168 , CYS B:1170 , CYS B:1175binding site for residue ZN B 1504
11AD2SOFTWAREMET B:1048 , TRP B:1050 , SER B:1084 , TYR B:1085 , ARG B:1109 , PHE B:1110 , ASN B:1112 , HIS B:1113 , TYR B:1154 , PHE B:1158 , PHE B:1166 , THR B:1167 , CYS B:1168 , GLN B:1169 , HOH B:1634 , HOH B:1659 , HOH B:1667 , HOH B:1722 , HOH B:1737 , HOH B:1771binding site for residue SAM B 1505
12AD3SOFTWAREASP B:1074 , ALA B:1077 , ASP B:1078 , ARG B:1080 , ASP B:1083 , LEU B:1086 , ASP B:1088 , VAL B:1096 , TYR B:1097 , CYS B:1098 , ARG B:1157 , PHE B:1158binding site for residue 9HJ B 1506

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VSC)

(-) 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:269
                                                                                                                                                                                                                                                                                                              
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.............eee...........ee....ee........hhhhh.............hhhhhh.......................ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhh.......eeee...eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh..............hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vsc A  918 TEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQSRLA 1190
                                   927       937       947       957       967       977       987       997      1007      1017      1027      1037      1047      1057      1067      1077      1087  ||  1101      1111      1121      1131      1141      1151      1161      1171      1181         
                                                                                                                                                                                                     1090|                                                                                               
                                                                                                                                                                                                      1095                                                                                               


Chain B from PDB  Type:PROTEIN  Length:272
                                                                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee.............eee...........ee....ee........hhhhh.............hhhhhh.......................ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhh.......eeee....eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh..............hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vsc B  916 IRTEKIICRDVARGYENVPIPCVNGVDGEPCPEDYKYISENCETSTMNIDRNITHLQHCTCVDDCSSSNCLCGQLSIRCWYDKDGRLLQEFNKIEPPLIFECNQACSCWRNCKNRVVQSGIKVRLQLYRTAKMGWGVRALQTIPQGTFICEYVGELISDAEADVREDDSYLFDLDGEVYCIDARYYGNISRFINHLCDPNIIPVRVFMLHQDLRFPRIAFFSSRDIRTGEELGFDYGDRFWDIKSKYFTCQCGSEKCKHSAEAIALEQSRLA 1190
                                   925       935       945       955       965       975       985       995      1005      1015      1025      1035      1045      1055      1065      1075      1085    ||1098      1108      1118      1128      1138      1148      1158      1168      1178      1188  
                                                                                                                                                                                                       1090|                                                                                                
                                                                                                                                                                                                        1094
   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 5VSC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5VSC)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    9HJ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SAM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5vsc)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5vsc
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  EHMT2_HUMAN | Q96KQ7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.1.1.43
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  EHMT2_HUMAN | Q96KQ7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        EHMT2_HUMAN | Q96KQ7: 2o8j 3dm1 3k5k 3rjw 4nvq 5jhn 5jin 5jiy 5jj0 5t0k 5t0m 5ttf 5tuy

(-) Related Entries Specified in the PDB File

5vsd 5vse 5vsf