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(-) Description

Title :  CRYSTAL STRUCTURE OF CATALYTIC DOMAIN OF GLP WITH MS012
 
Authors :  A. Dong, H. Zeng, J. Liu, Y. Xiong, N. Babault, J. Jin, W. Tempel, C. Bount C. H. Arrowsmith, A. M. Edwards, H. Wu, P. J. Brown, Structural Genomi Consortium (Sgc)
Date :  03 Nov 16  (Deposition) - 01 Feb 17  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Ehmt1, Glp, Ms012, Methyltransferase, Structural Genomics, Structural Genomics Consortium, Sgc, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. Zeng, A. Dong, J. Liu, Y. Xiong, N. Babault, J. Jin, W. Tempel, C. Bountra, C. H. Arrowsmith, A. M. Edwards, H. Wu, P. J. Brown
Crystal Structure Of Catalytic Domain Of Glp With Ms012
To Be Published
PubMed: search

(-) 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: PET28-LIC
    Expression System Strain: BL21-V2R-PRARE2
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 879-1159
    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 Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 30)

Asymmetric Unit (7, 30)
No.NameCountTypeFull Name
17KZ2Ligand/IonN4-(1-METHYLPIPERIDIN-4-YL)-N2-HEXYL-6,7-DIMETHOXYQUINAZOLINE-2,4-DIAMINE
2CL1Ligand/IonCHLORIDE ION
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4GOL1Ligand/IonGLYCEROL
5SAM2Ligand/IonS-ADENOSYLMETHIONINE
6UNX15Ligand/IonUNKNOWN ATOM OR ION
7ZN8Ligand/IonZINC ION
Biological Unit 1 (4, 9)
No.NameCountTypeFull Name
17KZ1Ligand/IonN4-(1-METHYLPIPERIDIN-4-YL)-N2-HEXYL-6,7-DIMETHOXYQUINAZOLINE-2,4-DIAMINE
2CL-1Ligand/IonCHLORIDE ION
3DMS-1Ligand/IonDIMETHYL SULFOXIDE
4GOL1Ligand/IonGLYCEROL
5SAM1Ligand/IonS-ADENOSYLMETHIONINE
6UNX6Ligand/IonUNKNOWN ATOM OR ION
7ZN-1Ligand/IonZINC ION
Biological Unit 2 (4, 12)
No.NameCountTypeFull Name
17KZ1Ligand/IonN4-(1-METHYLPIPERIDIN-4-YL)-N2-HEXYL-6,7-DIMETHOXYQUINAZOLINE-2,4-DIAMINE
2CL-1Ligand/IonCHLORIDE ION
3DMS1Ligand/IonDIMETHYL SULFOXIDE
4GOL-1Ligand/IonGLYCEROL
5SAM1Ligand/IonS-ADENOSYLMETHIONINE
6UNX9Ligand/IonUNKNOWN ATOM OR ION
7ZN-1Ligand/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:1443 , HOH A:1492 , HOH A:1522 , HOH A:1532 , HOH A:1535 , HOH A:1608 , HOH A:1621binding site for residue SAM A 1301
02AC2SOFTWAREALA 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 7KZ A 1302
03AC3SOFTWARECYS A:1062 , CYS A:1075 , CYS A:1105 , CYS A:1109binding site for residue ZN A 1303
04AC4SOFTWARECYS A:1068 , CYS A:1105 , CYS A:1111 , CYS A:1115binding site for residue ZN A 1304
05AC5SOFTWARECYS A:1062 , CYS A:1064 , CYS A:1068 , CYS A:1073binding site for residue ZN A 1305
06AC6SOFTWARECYS A:1203 , CYS A:1256 , CYS A:1258 , CYS A:1263binding site for residue ZN A 1306
07AC7SOFTWAREVAL A:1119 , ASN A:1122 , ARG A:1125 , LYS B:1262 , HOH B:1435binding site for residue CL A 1307
08AC8SOFTWAREASN A:1044 , LEU A:1159 , LEU A:1177 , HIS A:1216 , PHE A:1221 , PRO A:1222 , ARG A:1223binding site for residue GOL A 1308
09AC9SOFTWAREMET 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 , PHE B:1246 , CYS B:1256 , ARG B:1257 , HOH B:1420 , HOH B:1442 , HOH B:1492 , HOH B:1536 , HOH B:1591binding site for residue SAM B 1301
10AD1SOFTWAREALA B:1165 , ASP B:1166 , ARG B:1168 , ASP B:1171 , LEU B:1174 , ASP B:1176 , CYS B:1186 , ARG B:1245 , PHE B:1246 , ILE B:1249 , LYS B:1250binding site for residue 7KZ B 1302
11AD2SOFTWARECYS B:1062 , CYS B:1075 , CYS B:1105 , CYS B:1109binding site for residue ZN B 1303
12AD3SOFTWARECYS B:1068 , CYS B:1105 , CYS B:1111 , CYS B:1115binding site for residue ZN B 1304
13AD4SOFTWARECYS B:1062 , CYS B:1064 , CYS B:1068 , CYS B:1073binding site for residue ZN B 1305
14AD5SOFTWARECYS B:1203 , CYS B:1256 , CYS B:1258 , CYS B:1263binding site for residue ZN B 1306
15AD6SOFTWARELEU A:1078 , CYS B:1064 , ILE B:1065 , ASP B:1066 , SER B:1070binding site for residue DMS B 1307

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5TTG)

(-) 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:260
                                                                                                                                                                                                                                                                                                     
               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.......eee.......eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5ttg A 1006 VERIVSRDIARGYERIPIPCVNAVDSEPCPSNYKYVSQNCVTSPMNIDRNITHLQYCVCIDDCSSSNCMCGQLSMRCWYDKDGRLLPEFNMAEPPLIFECNHACSCWRNCRNRVVQNGLRARLQLYRTRDMGWGVRSLQDIPPGTFVCEYVGELISDSEADVREEDSYLFDLDNDGEVYCIDARFYGNVSRFINHHCEPNLVPVRVFMAHQDLRFPRIAFFSTRLIEAGEQLGFDYGERFWDIKGKLFSCRCGSPKCRHS 1266
                                  1015      1025      1035      1045      1055      1065      1075      1085      1095      1105      1115      1125      1135      1145      1155      1165      1175   || 1186      1196      1206      1216      1226      1236      1246      1256      1266
                                                                                                                                                                                                      1179|                                                                                     
                                                                                                                                                                                                       1181                                                                                     


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.......eee.....eeeeeeeee.hhhhhee.....eeeeeee.........eeeeee..........ee..hhhhhhhhh............... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5ttg 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)
  - → 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 5TTG)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

Asymmetric Unit(hide GO term definitions)

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        EHMT1_HUMAN | Q9H9B1: 2igq 2rfi 3b7b 3b95 3fpd 3hna 3mo0 3mo2 3mo5 3sw9 3swc 4i51 5tuz 5vsd 5vsf

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5ttf