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(-) Description

Title :  CO-CRYSTAL STRUCTURE OF HUMAN SMYD3 WITH AN AZA-SAH COMPOUND
 
Authors :  P. A. Elkins, W. G. Bonnette
Date :  11 Jan 16  (Deposition) - 30 Mar 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A
Keywords :  Smyd3, Methyltransferase, Oncology, Inhibitor, Transferase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. S. Van Aller, A. P. Graves, P. A. Elkins, W. G. Bonnette, P. J. Mcdevitt, F. Zappacosta, R. S. Annan, T. W. Dean, D. S. Su, C. L. Carpenter, H. P. Mohammad, R. G. Kruger
Structure-Based Design Of A Novel Smyd3 Inhibitor That Bridges The Sam-And Mekk2-Binding Pockets.
Structure V. 24 774 2016
PubMed-ID: 27066749  |  Reference-DOI: 10.1016/J.STR.2016.03.010

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SMYD3
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: UNIDENTIFIED BACULOVIRUS
    Expression System Strain: SF9
    Expression System Taxid: 10469
    Gene: SMYD3, ZMYND1, ZNFN3A1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: SET AND MYND DOMAIN-CONTAINING PROTEIN 3,ZINC FINGER MYND DOMAIN-CONTAINING PROTEIN 1

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
162X1Ligand/Ion5'-{[(3S)-3-AMINO-3-CARBOXYPROPYL][3-(DIMETHYLAMINO)PROPYL]AMINO}-5'-DEOXYADENOSINE
2DMS1Ligand/IonDIMETHYL SULFOXIDE
3MG2Ligand/IonMAGNESIUM ION
4ZN3Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:208 , CYS A:261 , CYS A:263 , CYS A:266binding site for residue ZN A 501
2AC2SOFTWARECYS A:62 , CYS A:65 , HIS A:83 , CYS A:87binding site for residue ZN A 502
3AC3SOFTWARECYS A:49 , CYS A:52 , CYS A:71 , CYS A:75binding site for residue ZN A 503
4AC4SOFTWAREHOH A:604 , HOH A:612 , HOH A:626 , HOH A:677 , HOH A:695 , HOH A:701binding site for residue MG A 504
5AC5SOFTWAREASP A:332 , GLN A:372 , HOH A:605 , HOH A:606 , HOH A:621 , HOH A:713binding site for residue MG A 505
6AC6SOFTWAREASN A:187 , MET A:190 , PRO A:367 , VAL A:368 , HOH A:669binding site for residue DMS A 506
7AC7SOFTWAREARG A:14 , ASN A:16 , TYR A:124 , GLU A:130 , ASN A:132 , LYS A:135 , CYS A:180 , ASN A:181 , SER A:182 , PHE A:183 , SER A:202 , ASN A:205 , HIS A:206 , TYR A:239 , TYR A:257 , PHE A:259 , HOH A:609 , HOH A:623 , HOH A:644 , HOH A:667 , HOH A:670binding site for residue 62X A 507

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HI7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Lys A:94 -Pro A:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HI7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HI7)

(-) Exons   (0, 0)

(no "Exon" information available for 5HI7)

(-) 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:426
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.....eeeee........eeeee...eeee...................ee.......ee.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..hhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhheeee.....eeeeee..hhhhhee.....eeeeee..eeeeee..........ee.......hhhhhhhhhhhh......hhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hi7 A   3 PLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS 428
                                    12        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
   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 5HI7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HI7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HI7)

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)

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  5hi7
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  SMYD3_HUMAN | Q9H7B4
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 Related Entries

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

UniProtKB/Swiss-Prot
        SMYD3_HUMAN | Q9H7B4: 3mek 3oxf 3oxg 3oxl 3pdn 3qwp 3ru0 5ccl 5ccm 5ex0 5ex3 5hq8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5HI7)