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(-) Description

Title :  STRUCTURE OF HUMAN GLP SET-DOMAIN (EHMT1) 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 :  1.85
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 EHMT1
    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: GLP CATALYTIC SET-DOMAIN RESIDUES 1006-1266
    Gene: EHMT1, EUHMTASE1, GLP, KIAA1876, KMT1D
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: EUCHROMATIC HISTONE-LYSINE N-METHYLTRANSFERASE 1,EU-HMTASE1, G9A-LIKE PROTEIN 1,GLP1,HISTONE H3-K9 METHYLTRANSFERASE 5,H3-K9- HMTASE 5,LYSINE N-METHYLTRANSFERASE 1D

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 15)

Asymmetric/Biological Unit (5, 15)
No.NameCountTypeFull Name
19HJ2Ligand/Ion6,7-DIMETHOXY-N~2~-METHYL-N~4~-(1-METHYLPIPERIDIN-4-YL)-N~2~-PROPYLQUINAZOLINE-2,4-DIAMINE
2DIO1Ligand/Ion1,4-DIETHYLENE DIOXIDE
3GOL2Ligand/IonGLYCEROL
4SAM2Ligand/IonS-ADENOSYLMETHIONINE
5ZN8Ligand/IonZINC ION

(-) Sites  (15, 15)

Asymmetric Unit (15, 15)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREMET A:1136 , GLY A:1137 , TRP A:1138 , SER A:1172 , TYR A:1173 , ARG A:1197 , PHE A:1198 , ASN A:1200 , HIS A:1201 , TYR A:1242 , PHE A:1246 , CYS A:1256 , ARG A:1257 , HOH A:3125 , HOH A:3177 , HOH A:3202 , HOH A:3226 , HOH A:3261 , HOH A:3287binding site for residue SAM A 3001
02AC2SOFTWARECYS A:1062 , CYS A:1075 , CYS A:1105 , CYS A:1109binding site for residue ZN A 3002
03AC3SOFTWARECYS A:1068 , CYS A:1105 , CYS A:1111 , CYS A:1115binding site for residue ZN A 3003
04AC4SOFTWARECYS A:1062 , CYS A:1064 , CYS A:1068 , CYS A:1073binding site for residue ZN A 3004
05AC5SOFTWARECYS A:1203 , CYS A:1256 , CYS A:1258 , CYS A:1263binding site for residue ZN A 3005
06AC6SOFTWAREASP A:1162 , ALA A:1165 , ASP A:1166 , ARG A:1168 , ASP A:1171 , LEU A:1174 , ASP A:1176 , CYS A:1186 , ARG A:1245 , PHE A:1246 , ILE A:1249 , LYS A:1250binding site for residue 9HJ A 3006
07AC7SOFTWARECYS A:1064 , ILE A:1065 , ASP A:1066 , ASN A:1072 , LEU B:1078 , PHE B:1103binding site for residue DIO A 3007
08AC8SOFTWAREMET B:1136 , GLY B:1137 , TRP B:1138 , SER B:1172 , TYR B:1173 , ARG B:1197 , PHE B:1198 , ASN B:1200 , HIS B:1201 , TYR B:1242 , CYS B:1256 , ARG B:1257 , HOH B:3216 , HOH B:3222 , HOH B:3249 , HOH B:3263 , HOH B:3285binding site for residue SAM B 3001
09AC9SOFTWARECYS B:1062 , CYS B:1075 , CYS B:1105 , CYS B:1109binding site for residue ZN B 3002
10AD1SOFTWARECYS B:1068 , CYS B:1105 , CYS B:1111 , CYS B:1115 , ZN B:3004binding site for residue ZN B 3003
11AD2SOFTWARECYS B:1062 , CYS B:1064 , CYS B:1068 , CYS B:1073 , ZN B:3003binding site for residue ZN B 3004
12AD3SOFTWARECYS B:1203 , CYS B:1256 , CYS B:1258 , CYS B:1263binding site for residue ZN B 3005
13AD4SOFTWAREALA B:1165 , ASP B:1166 , ARG B:1168 , ASP B:1171 , LEU B:1174 , ASP B:1176 , ARG B:1245 , PHE B:1246 , ILE B:1249 , LYS B:1250binding site for residue 9HJ B 3006
14AD5SOFTWAREHOH A:3159 , HOH A:3260 , ARG B:1054binding site for residue GOL B 3007
15AD6SOFTWAREASN B:1044 , LEU B:1159 , LEU B:1177 , HIS B:1216 , PHE B:1221 , PRO B:1222 , ARG B:1223 , HOH B:3254binding site for residue GOL B 3008

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5VSD)

(-) 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:257
                                                                                                                                                                                                                                                                                                  
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeee.............eee...........ee..............hhhhh.............hhhhhh.......................ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhh.......eee....eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5vsd A 1006 VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCRHS 1266
                                  1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175  ||  1189      1199      1209      1219      1229      1239      1249      1259       
                                                                                                                                                                                                     1178|                                                                                   
                                                                                                                                                                                                      1183                                                                                   


Chain B from PDB  Type:PROTEIN  Length:258
                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee.............eee...........ee..............hhhhh.............hhhhhhh......................ee...............hhhhh....eeeee.....eeeee........eeeee.eeeeehhhhh.......eeee....eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5vsd B 1006 VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCRHS 1266
                                  1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175  ||  1188      1198      1208      1218      1228      1238      1248      1258        
                                                                                                                                                                                                     1178|                                                                                    
                                                                                                                                                                                                      1182
   Legend:   → Mismatch (orange background)
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    → 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 5VSD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

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

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  EHMT1_HUMAN | Q9H9B1
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 Related Entries

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

UniProtKB/Swiss-Prot
        EHMT1_HUMAN | Q9H9B1: 2igq 2rfi 3b7b 3b95 3fpd 3hna 3mo0 3mo2 3mo5 3sw9 3swc 4i51 5ttg 5tuz 5vsf

(-) Related Entries Specified in the PDB File

5vsc 5vse 5vsf