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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN SMYD3 IN COMPLEX WITH A MAP3K2 PEPTIDE
 
Authors :  W. Fu, N. Liu, Q. Qiao, M. Wang, J. Min, B. Zhu, R. M. Xu, N. Yang
Date :  23 Nov 15  (Deposition) - 09 Mar 16  (Release) - 25 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Set Domain, Methylation, Chromatin, Cancer, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. Fu, N. Liu, Q. Qiao, M. Wang, J. Min, B. Zhu, R. M. Xu, N. Yang
Structural Basis For Substrate Preference Of Smyd3, A Set Domain-Containing Protein Lysine Methyltransferase
J. Biol. Chem. V. 291 9173 2016
PubMed-ID: 26929412  |  Reference-DOI: 10.1074/JBC.M115.709832

(-) Compounds

Molecule 1 - HISTONE-LYSINE N-METHYLTRANSFERASE SMYD3
    Chains: A
    EC Number: 2.1.1.43
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28A-SMT
    Expression System Strain: BL21(DE3) CODON PLUS RIL
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SMYD3, ZMYND1, ZNFN3A1
    Mutation: YES
    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 - MAP3K2 PEPTIDE
    Chains: D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1ACY2Ligand/IonACETIC ACID
2SAH1Ligand/IonS-ADENOSYL-L-HOMOCYSTEINE
3ZN3Ligand/IonZINC ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:49 , CYS A:52 , CYS A:71 , CYS A:75binding 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:208 , CYS A:261 , CYS A:263 , CYS A:266binding site for residue ZN A 503
4AC4SOFTWAREARG A:14 , GLY A:15 , ASN A:16 , TYR A:124 , ASN A:132 , CYS A:180 , ASN A:181 , SER A:202 , LEU A:203 , LEU A:204 , ASN A:205 , HIS A:206 , TYR A:239 , TYR A:257 , PHE A:259 , HOH A:618 , LYS D:260binding site for residue SAH A 504
5AC5SOFTWAREARG A:359 , ARG A:369 , HOH A:679binding site for residue ACY A 505
6AC6SOFTWAREGLN A:152 , ILE A:159 , LEU A:165binding site for residue ACY A 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5EX0)

(-) 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 5EX0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5EX0)

(-) Exons   (0, 0)

(no "Exon" information available for 5EX0)

(-) 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:429
                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               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....hhhhhhhhhhhheeeee.....eeeeee..hhhhhee.....eeeeee..eeeeee..........ee.......hhhhhhhhhhhhhh....hhhhhh..hhhhhh..hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ex0 A   0 FMEPLKVEKFATANRGNGLRAVTPLRPGELLFRSDPLAYTVCKGSRGVVCDRCLLGKEKLMRCSQCRVAKYCSAKCQKKAWPDHKRECKCLKSCKPRYPPDSVRLLGRVVFKLMDGAPSESEKLYSFYDLESNINKLTEDRKEGLRQLVMTFQHFMREEIQDASQLPPAFDLFEAFAKVICNSFTICNAEMQEVGVGLYPSISLLNHSCDPNCSIVFNGPHLLLRAVRDIEVGEELTICYLDMLMTSEERRKQLRDQYCFECDCFRCQTQDKDADMLTGDEQVWKEVQESLKKIEELKAHWKWEQVLAMCQAIISSNSERLPDINIYQLKVLDCAMDACINLGLLEEALFYGTRTMEPYRIFFPGSHPVRGVQVMKVGKLQLHQGMFPQAMKNLRLAFDIMRVTHGREHSLIEDLILLLEECDANIRAS 428
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419         


Chain D 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
                 5ex0 D 257 KFGKGGTYP 265
   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 5EX0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5EX0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5EX0)

(-) Gene Ontology  (37, 42)

Asymmetric/Biological Unit(hide GO term definitions)

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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
        M3K2_HUMAN | Q9Y2U5: 2cu1 2npt 5hq8
        SMYD3_HUMAN | Q9H7B4: 3mek 3oxf 3oxg 3oxl 3pdn 3qwp 3ru0 5ccl 5ccm 5ex3 5hi7 5hq8

(-) Related Entries Specified in the PDB File

5ex3