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(-) Description

Title :  CO-CRYSTAL STRUCTURE OF HUMAN SMYD3 WITH A MEKK2 PEPTIDE AT 2.13A
 
Authors :  P. A. Elkins, W. G. Bonnette
Date :  21 Jan 16  (Deposition) - 30 Mar 16  (Release) - 18 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.72
Chains :  Asym. Unit :  A,B,I,J
Biol. Unit 1:  A,I  (1x)
Biol. Unit 2:  B,J  (1x)
Keywords :  Smyd3, Methyltransferase, Oncology, Transferase (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, B
    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
 
Molecule 2 - MEKK2 PEPTIDE
    Chains: I, J
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABIJ
Biological Unit 1 (1x): A I 
Biological Unit 2 (1x):  B J

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 17)

Asymmetric Unit (5, 17)
No.NameCountTypeFull Name
1EDO6Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4SAH2Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
5ZN6Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2GOL-1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2GOL1Ligand/IonGLYCEROL
3MG-1Ligand/IonMAGNESIUM ION
4SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
5ZN-1Ligand/IonZINC ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:208 , CYS A:261 , CYS A:263 , CYS A:266binding site for residue ZN A 501
02AC2SOFTWARECYS A:62 , CYS A:65 , HIS A:83 , CYS A:87binding site for residue ZN A 502
03AC3SOFTWARECYS A:49 , CYS A:52 , CYS A:71 , CYS A:75binding site for residue ZN A 503
04AC4SOFTWAREPRO A:167 , PHE A:169 , HOH A:873 , HOH A:924binding site for residue MG A 504
05AC5SOFTWARELEU A:344 , HIS A:382 , GLN A:383binding site for residue EDO A 505
06AC6SOFTWARECYS A:238 , LEU A:240 , MET A:242 , HIS A:366 , HOH A:710 , GLY I:262 , TYR I:264binding site for residue EDO A 506
07AC7SOFTWAREARG A:14 , GLY A:15 , ASN A:16 , TYR A:124 , GLU A:130 , ASN A:132 , CYS A:180 , ASN A:181 , SER A:202 , LEU A:204 , ASN A:205 , HIS A:206 , TYR A:239 , TYR A:257 , PHE A:259 , HOH A:671 , HOH A:698 , HOH A:753 , HOH A:789 , HOH A:804 , HOH A:865 , HOH A:878 , LYS I:260binding site for residue SAH A 507
08AC8SOFTWARECYS B:208 , CYS B:261 , CYS B:263 , CYS B:266binding site for residue ZN B 501
09AC9SOFTWARECYS B:62 , CYS B:65 , HIS B:83 , CYS B:87binding site for residue ZN B 502
10AD1SOFTWARECYS B:49 , CYS B:52 , CYS B:71 , CYS B:75binding site for residue ZN B 503
11AD2SOFTWAREPRO B:167 , PHE B:169 , HOH B:766 , HOH B:848 , HOH B:852 , HOH B:853binding site for residue MG B 504
12AD3SOFTWARETHR B:184 , CYS B:186 , ILE B:214 , PHE B:216 , HOH B:649 , GLY J:261 , GLY J:262 , HOH J:401binding site for residue EDO B 505
13AD4SOFTWAREGLN B:152 , ILE B:159 , ALA B:162 , LEU B:171 , HOH B:607 , HOH B:616 , HOH B:786binding site for residue GOL B 506
14AD5SOFTWARECYS B:238 , LEU B:240 , MET B:242 , HIS B:366 , HOH B:762 , GLY J:262 , TYR J:264binding site for residue EDO B 507
15AD6SOFTWAREARG B:14 , ASN B:16 , TYR B:124 , ASN B:132 , CYS B:180 , ASN B:181 , SER B:202 , LEU B:204 , ASN B:205 , HIS B:206 , TYR B:239 , TYR B:257 , PHE B:259 , HOH B:611 , HOH B:638 , HOH B:642 , HOH B:716 , HOH B:721 , HOH B:763 , LYS J:260binding site for residue SAH B 508
16AD7SOFTWAREGLU A:192 , GLY I:261 , HOH I:405 , HOH I:406 , HOH I:407binding site for residue EDO I 301
17AD8SOFTWAREGLU B:192 , GLY J:261 , HOH J:405binding site for residue EDO J 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5HQ8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Lys A:94 -Pro A:95
2Lys B:94 -Pro B:95

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5HQ8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5HQ8)

(-) Exons   (0, 0)

(no "Exon" information available for 5HQ8)

(-) 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:426
                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeee.....eeeee........eeeee...eeee.hhhh..............ee.......ee.hhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh.....hhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhheeee.....eeeeee..hhhhhee.....eeeeee..eeeeee........eeee.......hhhhhhhhhhhhhh....hhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5hq8 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      


Chain B from PDB  Type:PROTEIN  Length:425
                                                                                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.....eeeee........eeeee...eeee.hhhh..............ee.......ee.hhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhhh.....hhhhh..hhhhh..hhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh....hhhhhhhhhhhhheeee.....eeeeee..hhhhhee.....eeeeee..eeeeee..........ee.......hhhhhhhhhhhhhh....hhhhhhh.hhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5hq8 B   3 PLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDKKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRA 427
                                    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     


Chain I from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .......... Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 5hq8 I 250 YEKFGKGGTY 264
                            ||     264
                          250|        
                           256        


Chain J from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author ......... Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 5hq8 J 256 EKFGKGGTY 264
   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 5HQ8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5HQ8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5HQ8)

(-) Gene Ontology  (37, 42)

Asymmetric Unit(hide GO term definitions)

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  SMYD3_HUMAN | Q9H7B4
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  2.1.1.43
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 Related Entries

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

UniProtKB/Swiss-Prot
        M3K2_HUMAN | Q9Y2U5: 2cu1 2npt 5ex0
        SMYD3_HUMAN | Q9H7B4: 3mek 3oxf 3oxg 3oxl 3pdn 3qwp 3ru0 5ccl 5ccm 5ex0 5ex3 5hi7

(-) Related Entries Specified in the PDB File

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