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(-) Description

Title :  CRYSTAL STRUCTURE OF PRMT5:MEP50 WITH COMPOUND 9 AND SINEFUNGIN
 
Authors :  P. A. Boriack-Sjodin, L. Jin
Date :  06 Nov 15  (Deposition) - 24 Feb 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.52
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (4x)
Keywords :  Protein-Inhibitor Complex, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. W. Duncan, N. Rioux, P. A. Boriack-Sjodin, M. J. Munchhoff, L. A. Reiter, C. R. Majer, L. Jin, L. D. Johnston, E. Chan-Penebre, K. G. Kuplast, M. Porter Scott, R. M. Pollock, N. J. Waters, J. J. Smith M. P. Moyer, R. A. Copeland, R. Chesworth
Structure And Property Guided Design In The Identification Of Prmt5 Tool Compound Epz015666
Acs Med. Chem. Lett. V. 7 162 2015
PubMed: search  |  Reference-DOI: 10.1021/ACSMEDCHEMLETT.5B00380

(-) Compounds

Molecule 1 - PROTEIN ARGININE N-METHYLTRANSFERASE 5
    ChainsA
    EC Number2.1.1.-, 2.1.1.125
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System PlasmidPDEST
    Expression System Taxid7108
    Expression System Vector TypeBACMID
    GenePRMT5, HRMT1L5, IBP72, JBP1, SKB1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    Synonym72 KDA ICLN-BINDING PROTEIN,HISTONE-ARGININE N- METHYLTRANSFERASE PRMT5,JAK-BINDING PROTEIN 1,SHK1 KINASE-BINDING PROTEIN 1 HOMOLOG,SKB1HS
 
Molecule 2 - METHYLOSOME PROTEIN 50
    ChainsB
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Cell LineSF9
    Expression System PlasmidPDEST
    Expression System Taxid7108
    Expression System Vector TypeBACMID
    GeneWDR77, MEP50, WD45, HKMT1069, NBLA10071
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymMEP-50,ANDROGEN RECEPTOR COFACTOR P44,WD REPEAT-CONTAINING PROTEIN 77,P44/MEP50

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (4x)AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
15QH1Ligand/Ion~{N}-[(2~{S})-3-(3,4-DIHYDRO-1~{H}-ISOQUINOLIN-2-YL)-2-OXIDANYL-PROPYL]-3-PYRIDIN-2-YL-BENZAMIDE
2GOL2Ligand/IonGLYCEROL
3SFG1Ligand/IonSINEFUNGIN
Biological Unit 1 (3, 16)
No.NameCountTypeFull Name
15QH4Ligand/Ion~{N}-[(2~{S})-3-(3,4-DIHYDRO-1~{H}-ISOQUINOLIN-2-YL)-2-OXIDANYL-PROPYL]-3-PYRIDIN-2-YL-BENZAMIDE
2GOL8Ligand/IonGLYCEROL
3SFG4Ligand/IonSINEFUNGIN

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:324 , LYS A:333 , TYR A:334 , GLY A:365 , ALA A:366 , GLY A:367 , PRO A:370 , LEU A:371 , GLU A:392 , LYS A:393 , SER A:418 , ASP A:419 , MET A:420 , GLU A:435 , LEU A:436 , CYS A:449 , 5QH A:702 , HOH A:830binding site for residue SFG A 701
2AC2SOFTWAREPHE A:300 , TYR A:304 , GLN A:309 , SER A:310 , PRO A:311 , LEU A:312 , LEU A:319 , PHE A:327 , LYS A:333 , GLU A:435 , LEU A:437 , GLY A:438 , SER A:439 , GLU A:444 , VAL A:503 , SER A:578 , TRP A:579 , PHE A:580 , SFG A:701 , HOH A:813 , HOH A:824 , HOH A:828binding site for residue 5QH A 702
3AC3SOFTWAREPHE A:40 , THR A:80 , TRP A:152 , GLN A:263binding site for residue GOL A 703
4AC4SOFTWAREASN A:295 , TYR A:297 , HIS A:572 , PRO A:574 , GLY A:575binding site for residue GOL A 704

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1B:208 -B:247

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Glu A:57 -Pro A:58
2Gly A:64 -Pro A:65
3Ile A:464 -Pro A:465
4His A:523 -Pro A:524
5Ala A:619 -Pro A:620
6Ala B:67 -Pro B:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EMK)

(-) 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:625
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.....hhhhhhhhhhhh...eeeee.............hhhhh......hhhhhhhhhhhhheeee..........hhhhhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh......eeeeeee..hhhhh...................hhhhhhhhhhhhhh.....eeeeee......hhhhhhh.....eeeeeee.hhhee.....ee.hhhhhhhhhhhhhh..eeeee.........hhhhhhhhhhhhhh....hhhhhhhhhhh..............hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...eeeeeee....hhhhhhhhhhhh....eeeeeee..hhhhhhhhhhhhhhhhhh.eeee............eeeeee..........hhhhhhhhhhh.eeeeeeee..eeeeeeeeeehhhhhhhhhh........hhhhhh.ee......ee....eeeeeee...........eeeeeeee....eeeeeeeeeeeeeee..eeee.hhhhh.........eeeeeeeeeee....eeeeeeeeee...eeeeeeeeee.......hhhhh...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5emk A  13 RVSSGRDLNCVPEIADTLGAVAKQGFDFLCMPVFHPRFKREFIQEPAKNRPGPQTRSDLLLSGRDWNTLIVGKLSPWIRPDSKVEKIRRNSEAAMLQELNFGAYLGLPAFLLPLNQEDNTNLARVLTNHIHTGHHSSMFWMRVPLVAPEDLRDDIIENAPTTHTEEYSGEEKTWMWWHNFRTLCDYSKRIAVALEIGADLPSNHVIDRWLGEPIKAAILPTSIFLTNKKGFPVLSKMHQRLIFRLLKLEVQFIITGTNHHSEKEFCSYLQYLEYLSQNRPPPNAYELFAKGYEDYLQSPLQPLMDNLESQTYEVFEKDPIKYSQYQQAIYKCLLDRVPEEEKDTNVQVLMVLGAGRGPLVNASLRAAKQADRRIKLYAVEKNPNAVVTLENWQFEEWGSQVTVVSSDMREWVAPEKADIIVSELLGSFADNELSPECLDGAQHFLKDDGVSIPGEYTSFLAPISSSKLYNEVRACREKDRDPEAQFEMPYVVRLHNFHQLSAPQPCFTFSHPNRDPMIDNNRYCTLEFPVEVNTVLHGFAGYFETVLYQDITLSIRPETHSPGMFSWFPILFPIKQPITVREGQTICVRFWRCSNSKKVWYEWAVTAPVCSAIHNPTGRSYTIGL 637
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632     

Chain B from PDB  Type:PROTEIN  Length:313
                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeee.....eeeeee........eeeeee.hhhhh.......eeeee...eeeeeee...eeeeee...eeeeeee......eeeeeeee.....eeeeee.....eeeeee....eeeee....eeeeee......eeeeee......eeeeee....eeeee......eee.........eeeeee......eeeeee...eeeeee.......eeee.....eeeeee.......eeeee....eeee.....eeeee......eeeeee......eeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5emk B  16 EWNLPPNAPACMERQLEAARYRSDGALLLGASSLSGRCWAGSLWLFKDPCAAPNEGFCSAGVQTEAGVADLTWVGERGILVASDSGAVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDICIKVWDLAQQVVLSSYRAHAAQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQIGCSAPGYLPTSLAWHPQQSEVFVFGDENGTVSLVDTKSTSCVLSSAVHSQCVTGLVFSPHSVPFLASLSEDCSLAVLDSSLSELFRSQAHRDFVRDATWSPLNHSLLTTVGWDHQVVHHVVP 328
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325   

   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 5EMK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (51, 62)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        ANM5_HUMAN | O147444gqb 4x60 4x61 4x63 5c9z 5emj 5eml 5emm 5fa5
        MEP50_HUMAN | Q9BQA14gqb 4x60 4x61 4x63 5c9z 5emj 5eml 5emm 5fa5

(-) Related Entries Specified in the PDB File

5emj 5eml 5emm