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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN PROTEIN ARGININE METHYLTRANSFERASE PRMT6 BOUND TO SAH AND AN ARYL PYRAZOLE INHIBITOR
 
Authors :  K. K. Swinger, P. A. Boriack-Sjodin
Date :  09 Feb 15  (Deposition) - 22 Apr 15  (Release) - 08 Jul 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. H. Mitchell, A. E. Drew, S. A. Ribich, N. Rioux, K. K. Swinger, S. L. Jacques, T. Lingaraj, P. A. Boriack-Sjodin, N. J. Waters, T. J. Wigle, O. Moradei, L. Jin, T. Riera, M. Porter-Scott, M. P. Moyer, J. J. Smith, R. Chesworth, R. A. Copeland
Aryl Pyrazoles As Potent Inhibitors Of Arginine Methyltransferases: Identification Of The First Prmt6 Tool Compound.
Acs Med. Chem. Lett. V. 6 655 2015
PubMed-ID: 26101569  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00071

(-) Compounds

Molecule 1 - PROTEIN ARGININE N-METHYLTRANSFERASE 6
    ChainsA, B
    EC Number2.1.1.-, 2.1.1.125
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 27-375
    GenePRMT6, HRMT1L6
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN METHYLTRANSFERASE- LIKE PROTEIN 6,HISTONE-ARGININE N-METHYLTRANSFERASE PRMT6

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
149K2Ligand/IonN-{[5-(4-FLUOROPHENYL)-1H-PYRAZOL-4-YL]METHYL}-N-METHYLETHANE-1,2-DIAMINE
2GOL1Ligand/IonGLYCEROL
3SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:47 , TYR A:48 , TYR A:51 , MET A:60 , ARG A:66 , GLY A:90 , ALA A:91 , GLY A:92 , ILE A:95 , LEU A:96 , GLU A:112 , ALA A:113 , PRO A:139 , VAL A:140 , GLU A:141 , MET A:166 , SER A:169 , 49K A:402 , HOH A:554 , HOH A:555 , HOH A:561 , HOH A:638binding site for residue SAH A 401
2AC2SOFTWARETYR A:51 , VAL A:56 , GLU A:59 , GLU A:155 , MET A:157 , TYR A:159 , GLU A:164 , HIS A:317 , SAH A:401 , HOH A:564binding site for residue 49K A 402
3AC3SOFTWARETYR B:47 , TYR B:51 , MET B:60 , ARG B:66 , GLY B:90 , ALA B:91 , ILE B:95 , LEU B:96 , GLU B:112 , ALA B:113 , SER B:114 , PRO B:139 , VAL B:140 , GLU B:141 , GLU B:155 , MET B:166 , SER B:169 , 49K B:402 , HOH B:524 , HOH B:527 , HOH B:530 , HOH B:536 , HOH B:553binding site for residue SAH B 401
4AC4SOFTWARETYR B:51 , VAL B:56 , GLU B:59 , GLU B:155 , MET B:157 , TYR B:159 , GLU B:164 , HIS B:317 , TRP B:318 , SAH B:401 , HOH B:575binding site for residue 49K B 402
5AC5SOFTWARELEU B:162 , SER B:165 , LEU B:344 , PRO B:350 , ARG B:351 , ARG B:352 , LEU B:353 , HOH B:556 , HOH B:577binding site for residue GOL B 403

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Y2H)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Leu A:185 -Pro A:186
2Leu B:185 -Pro B:186

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y2H)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y2H)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y2H)

(-) 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:337
                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhh...eeeeee...hhhhhhhhhhhh.....eeeee...........eeeee............hhhhhhhhhhhheeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhh...eeeee..hhhhh....eeeeeee....hhhhhhhhheeeeeeee....eeeeeeeeeeeeee........eeee...........eeeeeeeeeeee....eeeeeeeeee.......eeeeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y2h A  39 TKRERDQLYYECYSDVSVHEEMIADRVRTDAYRLGILRNWAALRGKTVLDVGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRFNGLEDRVHVLPGPVETVELPEQVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPASAELFIAPISDQMLEWRLGFWSQVKQHYGVDMSCLEGFATRCLMGHSEIVVQGLSGEDVLARPQRFAQLELSRAGLEQELEAGVGGRFRCSCYGSAPMHGFAIWFQVTFPGGESEKPLVLSTSPFHPATHWKQALLYLNEPVQVEQDTDVSGEITLLPSRDNPRRLRVLLRYKVGDQEEKTKDFAMED 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 B from PDB  Type:PROTEIN  Length:352
                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee....hhhhhhhhhhh..eeeeee...hhhhhhhhhhhh.....eeeee...........eeeee............hhhhhhhhhhhheeeeeeee..eeeeeeeee.hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..eeeee..hhhhh....eeeeeee....hhhhhhhhheeeeeeee....eeeeeeeeeeeeee........eeee...........eeeeeeeeeeee....eeeeeeeeee.......eeeeeeeee.....eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y2h B  24 SIAAEREAALERPRRTKRERDQLYYECYSDVSVHEEMIADRVRTDAYRLGILRNWAALRGKTVLDVGAGTGILSIFCAQAGARRVYAVEASAIWQQAREVVRFNGLEDRVHVLPGPVETVELPEQVDAIVSEWMGYGLLHESMLSSVLHARTKWLKEGGLLLPASAELFIAPISDQMLEWRLGFWSQVKQHYGVDMSCLEGFATRCLMGHSEIVVQGLSGEDVLARPQRFAQLELSRAGLEQELEAGVGGRFRCSCYGSAPMHGFAIWFQVTFPGGESEKPLVLSTSPFHPATHWKQALLYLNEPVQVEQDTDVSGEITLLPSRDNPRRLRVLLRYKVGDQEEKTKDFAMED 375
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373  

   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 4Y2H)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y2H)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y2H)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)

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    Leu A:185 - Pro A:186   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        ANM6_HUMAN | Q96LA84hc4 4qpp 4qqk 4y30 5e8r 5egs 5hzm

(-) Related Entries Specified in the PDB File

4y30