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(-) Description

Title :  CRYSTAL STRUCTURE OF PRMT5:MEP50 WITH COMPOUND 8 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 :  2.27
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
    Chains: A
    EC Number: 2.1.1.-, 2.1.1.125
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Plasmid: PDEST
    Expression System Taxid: 7108
    Expression System Vector Type: BACMID
    Gene: PRMT5, HRMT1L5, IBP72, JBP1, SKB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 72 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
    Chains: B
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Cell Line: SF9
    Expression System Plasmid: PDEST
    Expression System Taxid: 7108
    Expression System Vector Type: BACMID
    Gene: WDR77, MEP50, WD45, HKMT1069, NBLA10071
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MEP-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, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
15QJ1Ligand/Ion(2~{S})-1-(3,4-DIHYDRO-1~{H}-ISOQUINOLIN-2-YL)-3-[[4-(3-METHYLBENZIMIDAZOL-5-YL)PYRIDIN-2-YL]AMINO]PROPAN-2-OL
2GOL4Ligand/IonGLYCEROL
3SFG1Ligand/IonSINEFUNGIN
Biological Unit 1 (3, 24)
No.NameCountTypeFull Name
15QJ4Ligand/Ion(2~{S})-1-(3,4-DIHYDRO-1~{H}-ISOQUINOLIN-2-YL)-3-[[4-(3-METHYLBENZIMIDAZOL-5-YL)PYRIDIN-2-YL]AMINO]PROPAN-2-OL
2GOL16Ligand/IonGLYCEROL
3SFG4Ligand/IonSINEFUNGIN

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:315 , TYR A:324 , LYS A:333 , TYR A:334 , GLY A:365 , 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 , 5QJ A:702 , HOH A:846 , HOH A:849 , HOH A:854binding site for residue SFG A 701
2AC2SOFTWAREPHE A:300 , TYR A:304 , LEU A:312 , LEU A:319 , PHE A:327 , LYS A:333 , GLU A:435 , LEU A:437 , GLU A:444 , VAL A:503 , SER A:578 , TRP A:579 , SFG A:701 , HOH A:823binding site for residue 5QJ A 702
3AC3SOFTWARETYR A:297 , GLY A:575 , HOH A:825binding site for residue GOL A 703
4AC4SOFTWAREPHE A:40 , THR A:80 , TRP A:152 , GLN A:263 , HOH A:844binding site for residue GOL A 704
5AC5SOFTWAREARG A:52 , GLU A:53 , LYS A:60 , GLN A:66 , GLN A:109binding site for residue GOL A 705
6AC6SOFTWAREASN B:190 , ILE B:192 , CYS B:208 , PRO B:211 , GLY B:212 , TYR B:213 , PHE B:230binding site for residue GOL B 401

(-) 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 5EMJ)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5EMJ)

(-) 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.....hhhhhhhhhhhhh..eeeee.............hhhhh......hhhhhhhhhhhhheeee..........hhhhhhhhhhhhhhhhhhhhhhh..eeeee.....hhhhhhhhhhhhh......eeeeeee.......................hhhhhhhhhhhhhhhhh.....eeeeee..........hhhhh...eeeeeee.hhhee.....ee.hhhhhhhhhhhhhhh.eeeee.........hhhhhhhhhhhhhh....hhhhhhhhhhh..ee..........hhhhhhhhhh..hhhhhhhhhhhhhhhhhh........eeeeeee....hhhhhhhhhhhhhhh.eeeeeeee.hhhhhhhhhhhhhhhhhh.eeeee...........eeeee...........hhhhhhhhhhh.eeeeeeee..eeeeeeeeeehhhhhhhhhh........hhhhhh.eee.....ee....eeeeeee...........eeeeeeee....eeeeeeeeeeeeeee..eeee.hhhhh.........eeeeeeeeeee....eeeeeeeeee...eeeeeeeeee.......hhhhh...ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5emj 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:303
                                                                                                                                                                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.....eeeeee........eeeeee.hhhhh.hhhhh.eeeee...eeeeeee...eeeeee...eeeeeee......eeeeeeee.....eeeeee.....eeeeee....eeeee....eeeeee......eeeeee......eeeeee....eeeee......eeee........eeeeee......eeeeee...eeeeee....eeeeeee.....eeeeee.......eeeee....eeee.....eeeee......eeeeee......eeeeee....eeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5emj B  26 CMERQLEAARYRSDGALLLGASSLSGRCWAGSLWLFKDPCAAPNEGFCSAGVQTEAGVADLTWVGERGILVASDSGAVELWELDENETLIVSKFCKYEHDDIVSTVSVLSSGTQAVSGSKDICIKVWDLAQQVVLSSYRAHAAQVTCVAASPHKDSVFLSCSEDNRILLWDTRCPKPASQIGCSAPGYLPTSLAWHPQQSEVFVFGDENGTVSLVDTKSTSCVLSSAVHSQCVTGLVFSPHSVPFLASLSEDCSLAVLDSSLSELFRSQAHRDFVRDATWSPLNHSLLTTVGWDHQVVHHVVP 328
                                    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)
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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 5EMJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (51, 62)

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  MEP50_HUMAN | Q9BQA1
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 Related Entries

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

UniProtKB/Swiss-Prot
        ANM5_HUMAN | O14744: 4gqb 4x60 4x61 4x63 5c9z 5emk 5eml 5emm 5fa5
        MEP50_HUMAN | Q9BQA1: 4gqb 4x60 4x61 4x63 5c9z 5emk 5eml 5emm 5fa5

(-) Related Entries Specified in the PDB File

5emk 5eml 5emm