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(-) Description

Title :  HUMAN PRMT6 WITH BOUND FRAGMENT-TYPE INHIBITOR
 
Authors :  H. Steuber, U. Egner, J. Kania, H. Wu, P. J. Brown
Date :  27 Oct 15  (Deposition) - 03 Feb 16  (Release) - 22 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Fragment, Inhibitor, Prmt, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Ferreira De Freitas, M. S. Eram, M. M. Szewczyk, H. Steuber, D. Smil, H. Wu, F. Li, G. Senisterra, A. Dong, P. J. Brown, M. Hitchcock, D. Moosmayer, C. M. Stegmann, U. Egner, C. Arrowsmith, D. Barsyte-Lovejoy, M. Vedadi, M. Schapira
Discovery Of A Potent Class I Protein Arginine Methyltransferase Fragment Inhibitor.
J. Med. Chem. V. 59 1176 2016
PubMed-ID: 26824386  |  Reference-DOI: 10.1021/ACS.JMEDCHEM.5B01772

(-) Compounds

Molecule 1 - PROTEIN ARGININE N-METHYLTRANSFERASE 6
    Chains: A, B, C, D
    EC Number: 2.1.1.-, 2.1.1.125
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Gene: PRMT6, HRMT1L6
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN METHYLTRANSFERASE- LIKE PROTEIN 6,HISTONE-ARGININE N-METHYLTRANSFERASE PRMT6

 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  (2, 10)

Asymmetric Unit (2, 10)
No.NameCountTypeFull Name
15NR6Ligand/Ion2-[4-(PHENYLMETHYL)PIPERIDIN-1-YL]ETHANAMINE
2SAH4Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 1 (2, 5)
No.NameCountTypeFull Name
15NR3Ligand/Ion2-[4-(PHENYLMETHYL)PIPERIDIN-1-YL]ETHANAMINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
Biological Unit 2 (2, 5)
No.NameCountTypeFull Name
15NR3Ligand/Ion2-[4-(PHENYLMETHYL)PIPERIDIN-1-YL]ETHANAMINE
2SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:47 , TYR A:48 , TYR A:51 , MET A:60 , ARG A:66 , GLY A:90 , ALA A:91 , LEU A:96 , GLU A:112 , ALA A:113 , PRO A:139 , VAL A:140 , GLU A:141 , GLU A:155 , MET A:166 , SER A:169 , 5NR A:402 , HOH A:510 , HOH A:513 , HOH A:538 , HOH A:549binding site for residue SAH A 401
02AC2SOFTWARECYS A:50 , TYR A:51 , VAL A:56 , MET A:60 , GLU A:155 , MET A:157 , TYR A:159 , GLU A:164 , HIS A:317 , TRP A:318 , SAH A:401 , HOH A:527binding site for residue 5NR A 402
03AC3SOFTWARELEU A:162 , SER A:165 , SER A:168 , GLU A:264 , LEU A:267 , LEU A:343 , LEU A:344 , PRO A:345binding site for residue 5NR A 403
04AC4SOFTWARETYR B:47 , TYR B:48 , TYR B:51 , MET B:60 , ARG B:66 , GLY B:90 , ALA B:91 , LEU B:96 , GLU B:112 , ALA B:113 , SER B:114 , GLY B:138 , PRO B:139 , VAL B:140 , GLU B:141 , GLU B:155 , MET B:166 , SER B:169 , 5NR B:402 , HOH B:517 , HOH B:548 , HOH B:561 , HOH B:563binding site for residue SAH B 401
05AC5SOFTWARETYR B:51 , VAL B:56 , GLU B:155 , MET B:157 , TYR B:159 , GLU B:164 , HIS B:317 , TRP B:318 , SAH B:401 , HOH B:565binding site for residue 5NR B 402
06AC6SOFTWARETYR C:47 , TYR C:48 , TYR C:51 , MET C:60 , ARG C:66 , GLY C:90 , ALA C:91 , GLY C:92 , ILE C:95 , LEU C:96 , GLU C:112 , ALA C:113 , SER C:114 , GLY C:138 , PRO C:139 , VAL C:140 , GLU C:141 , GLU C:155 , MET C:166 , SER C:169 , 5NR C:402 , HOH C:511 , HOH C:514 , HOH C:522 , HOH C:531binding site for residue SAH C 401
07AC7SOFTWARETYR C:51 , VAL C:56 , MET C:60 , GLU C:155 , MET C:157 , TYR C:159 , GLU C:164 , HIS C:317 , SAH C:401 , HOH C:519binding site for residue 5NR C 402
08AC8SOFTWARELEU C:162 , SER C:165 , SER C:168 , GLU C:264 , GLU C:268 , LEU C:343 , LEU C:344 , PRO C:345binding site for residue 5NR C 403
09AC9SOFTWARETYR D:47 , TYR D:51 , MET D:60 , ARG D:66 , GLY D:90 , ALA D:91 , GLY D:92 , ILE D:95 , LEU D:96 , GLU D:112 , ALA D:113 , SER D:114 , PRO D:139 , VAL D:140 , GLU D:141 , GLU D:155 , MET D:166 , SER D:169 , 5NR D:402 , HOH D:501 , HOH D:515 , HOH D:524binding site for residue SAH D 401
10AD1SOFTWARETYR D:51 , VAL D:56 , GLU D:155 , MET D:157 , TYR D:159 , GLU D:164 , HIS D:317 , TRP D:318 , SAH D:401 , HOH D:557binding site for residue 5NR D 402

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:185 -Pro A:186
2Leu B:185 -Pro B:186
3Leu C:185 -Pro C:186
4Leu D:185 -Pro D:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EGS)

(-) 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:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh...eeeeee...hhhhhhhhhhhh.....eeeee...........eeeee...........hhhhhhhhhhhhheeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..eeeee..hhhhh....eeeeeee....hhhhhhhhheeeeeeee....eeeeeeeeeeeeee......eeee...........eeeeeeeeeeee....eeeeeeeeee.......eeeeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5egs A  39 TKRERDQLYYECYSDVSVHEEMIADRVRTDAYRLGILRNWAALRGKTVLDVGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRFNGLEDRVHVLPGPVETVELPEQVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPASAELFIVPISDQMLEWRLGFWSQVKQHYGVDMSCLEGFATRCLMGHSEIVVQGLSGEDVLARPQRFAQLELSRAGLEQELEAGVGGRFRCSCYGSAPMHGFAIWFQVTFPGGEKPLVLSTSPFHPATHWKQALLYLNEPVQVEQDTDVSGEITLLPSRDNPRRLRVLLRYKVGDQEEKTKDFAMED 375
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298||     310       320       330       340       350       360       370     
                                                                                                                                                                                                                                                                                              299|                                                                         
                                                                                                                                                                                                                                                                                               302                                                                         


Chain B from PDB  Type:PROTEIN  Length:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh...eeeeee...hhhhhhhhhhhh.....eeeee...........eeeee...........hhhhhhhhhhhhheeeeeeee..eeeeeeeee.hhhhhhhhhh..hhhhhhh..hhhhhhhhhhhhhh..eeeee..hhhhh....eeeeeee....hhhhhhhhheeeeeeee....eeeeeeeeeeeeee........eeee...........eeeeeeeeeeee....eeeeeeeeee.......eeeeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5egs B  38 RTKRERDQLYYECYSDVSVHEEMIADRVRTDAYRLGILRNWAALRGKTVLDVGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRFNGLEDRVHVLPGPVETVELPEQVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPASAELFIVPISDQMLEWRLGFWSQVKQHYGVDMSCLEGFATRCLMGHSEIVVQGLSGEDVLARPQRFAQLELSRAGLEQELEAGVGGRFRCSCYGSAPMHGFAIWFQVTFPGGESEKPLVLSTSPFHPATHWKQALLYLNEPVQVEQDTDVSGEITLLPSRDNPRRLRVLLRYKVGDQEEKTKDFAMED 375
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367        


Chain C from PDB  Type:PROTEIN  Length:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh..eeeeee...hhhhhhhhhhhh.....eeeee...........eeeee...........hhhhhhhhhhhhheeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..eeeee..hhhhh....eeeeeee....hhhhhhhhheeeeeeee....eeeeeeeeeeeeee........eeee...........eeeeeeeeeeee....eeeeeeeeee.......eeeeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5egs C  39 TKRERDQLYYECYSDVSVHEEMIADRVRTDAYRLGILRNWAALRGKTVLDVGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRFNGLEDRVHVLPGPVETVELPEQVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPASAELFIVPISDQMLEWRLGFWSQVKQHYGVDMSCLEGFATRCLMGHSEIVVQGLSGEDVLARPQRFAQLELSRAGLEQELEAGVGGRFRCSCYGSAPMHGFAIWFQVTFPGGESEKPLVLSTSPFHPATHWKQALLYLNEPVQVEQDTDVSGEITLLPSRDNPRRLRVLLRYKVGDQEEKTKDFAMED 375
                                    48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       


Chain D from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh...eeeeee...hhhhhhhhhhhh.....eeeee...........eeeee...........hhhhhhhhhhhhheeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeee..hhhhh....eeeeeee....hhhhhhhhheeeeeeee....eeeeeeeeeeeeee....eeee...........eeeeeeeeeeee....eeeeeeeeee.......eeeeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5egs D  38 RTKRERDQLYYECYSDVSVHEEMIADRVRTDAYRLGILRNWAALRGKTVLDVGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRFNGLEDRVHVLPGPVETVELPEQVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPASAELFIVPISDQMLEWRLGFWSQVKQHYGVDMSCLEGFATRCLMGHSEIVVQGLSGEDVLARPQRFAQLELSRAGLEQELEAGVGGRFRCSCYGSAPMHGFAIWFQVTFPGGPLVLSTSPFHPATHWKQALLYLNEPVQVEQDTDVSGEITLLPSRDNPRRLRVLLRYKVGDQEEKTKDFAMED 375
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297 ||    311       321       331       341       351       361       371    
                                                                                                                                                                                                                                                                                               299|                                                                       
                                                                                                                                                                                                                                                                                                304
   Legend:   → Mismatch (orange background)
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  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 5EGS)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (32, 32)

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        ANM6_HUMAN | Q96LA8: 4hc4 4qpp 4qqk 4y2h 4y30 5e8r 5hzm

(-) Related Entries Specified in the PDB File

4qpp