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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN JMJD2C CATALYTIC DOMAIN IN COMPLEX 6-ETHYL-5-METHYL-7-OXO-4,7-DIHYDROPYRAZOLO(1,5-A) PYRIMIDINE-3-CARBONITRILE
 
Authors :  V. Cecatiello, S. Pasqualato
Date :  09 Oct 15  (Deposition) - 21 Oct 15  (Release) - 21 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.66
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, Transcription Regulation, Metal Binding, Demethylase, Lysine-Specific Demethylase 4C, (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  V. Cecatiello, S. Pasqualato
Crystal Structures Of Human Jmjd2C Catalytic Domain Bound To Inhibitors
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - LYSINE-SPECIFIC DEMETHYLASE 4C
    ChainsA
    EC Number1.14.11.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPETM14
    Expression System Taxid469008
    Expression System VariantPLYSS
    Expression System Vector TypePLASMID
    FragmentCATALYTIC DOMAIN, RESIDUES 3-347
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymJMJD2C, GENE AMPLIFIED IN SQUAMOUS CELL CARCINOMA 1 PROTEIN, GASC-1 PROTEIN, JMJC DOMAIN-CONTAINING HISTONE DEMETHYLATION PROTEIN 3C, JUMONJI DOMAIN-CONTAINING PROTEIN 2C

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 12)

Asymmetric/Biological Unit (5, 12)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2EDO5Ligand/Ion1,2-ETHANEDIOL
3EM61Ligand/Ion6-ETHYL-5-METHYL-7-OXIDANYLIDENE-1H-PYRAZOLO[1,5-A]PYRIMIDINE-3-CARBONITRILE
4NI1Ligand/IonNICKEL (II) ION
5ZN1Ligand/IonZINC ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARECYS A:236 , HIS A:242 , CYS A:308 , CYS A:310BINDING SITE FOR RESIDUE ZN A1348
02AC2SOFTWAREHIS A:190 , GLU A:192 , HIS A:278 , EM6 A:1350 , HOH A:2221 , HOH A:2227BINDING SITE FOR RESIDUE NI A1349
03AC3SOFTWARETYR A:134 , THR A:186 , PHE A:187 , HIS A:190 , ASN A:200 , LYS A:208 , HIS A:278 , ASN A:282 , NI A:1349 , HOH A:2221 , HOH A:2227 , HOH A:2346BINDING SITE FOR RESIDUE EM6 A1350
04AC4SOFTWAREARG A:112 , ASN A:126 , TRP A:183BINDING SITE FOR RESIDUE CL A1351
05AC5SOFTWARETYR A:179 , SER A:290BINDING SITE FOR RESIDUE CL A1352
06AC6SOFTWAREALA A:238 , PHE A:239 , LEU A:240 , HOH A:2264BINDING SITE FOR RESIDUE CL A1353
07AC7SOFTWAREPRO A:111 , ARG A:112BINDING SITE FOR RESIDUE CL A1354
08AC8SOFTWAREASN A:88 , GLN A:90 , EDO A:1356 , HOH A:2347 , HOH A:2348BINDING SITE FOR RESIDUE EDO A1355
09AC9SOFTWAREGLN A:90 , EDO A:1355BINDING SITE FOR RESIDUE EDO A1356
10BC1SOFTWARELYS A:56 , GLU A:149 , HOH A:2078 , HOH A:2349 , HOH A:2350BINDING SITE FOR RESIDUE EDO A1357
11BC2SOFTWARETYR A:116 , GLU A:117 , GLU A:120 , SER A:209 , LYS A:261 , HOH A:2288BINDING SITE FOR RESIDUE EDO A1358
12BC3SOFTWARELYS A:107 , GLN A:327 , PRO A:328 , ASP A:329 , HOH A:2335BINDING SITE FOR RESIDUE EDO A1359

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5FJK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FJK)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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Chain A from PDB  Type:PROTEIN  Length:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......eee..hhhhhhhhhhhhhhhhhhhhhhh.eeee...........hhhhhh.ee...eeeeeeee..eeeeeeee...eehhhhhhhhh..........hhhhhhhhhhhhh.....eeeeeee.................hhhhhhhhhhh.........eeeee....eeeee.hhhhheeeeeeeee..eeeeeehhhhhhhhhhhhhhhhhhhhhhh.hhhhhh.eeehhhhhhhhh...eeeee....eeee....eeeeee...eeeeeeee.hhhhhhhhhhh.............hhhhhhhhh..hhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fjk A  10 LNPSCKIMTFRPSMEEFREFNKYLAYMESKGAHRAGLAKVIPPKEWKPRQCYDDIDNLLIPAPIQQMVTGQSGLFTQYNIQKKAMTVKEFRQLANSGKYCTPRYLDYEDLERKYWKNLTFVAPIYGADINGSIYDEGVDEWNIARLNTVLDVVEEECGISIEGVNTPYLYFGMWKTTFAWHTEDMDLYSINYLHFGEPKSWYAIPPEHGKRLERLAQGFFPSSSQGCDAFLRHKMTLISPSVLKKYGIPFDKITQEAGEFMITFPYGYHAGFNHGFNCAESTNFATVRWIDYGKVAKLCTCRKDMVKISMDIFVRKFQPDRYQLWKQGKDIYTIDHTK 347
                                    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        

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  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 5FJK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (17, 17)

Asymmetric/Biological Unit(hide GO term definitions)

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        KDM4C_HUMAN | Q9H3R02xdp 2xml 4xdo 4xdp 5fjh 5kr7

(-) Related Entries Specified in the PDB File

5fjh CRYSTAL STRUCTURE OF HUMAN JMJD2C CATALYTIC DOMAIN IN COMPLEX WITH EPITHERAPUETIC COMPOUND 2-(((2-((2-( DIMETHYLAMINO)ETHYL) (ETHYL)AMINO)-2-OXOETHYL)AMINO) METHYL)ISONICOTINIC ACID